Starting phenix.real_space_refine on Tue Aug 26 06:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e96_47775/08_2025/9e96_47775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e96_47775/08_2025/9e96_47775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e96_47775/08_2025/9e96_47775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e96_47775/08_2025/9e96_47775.map" model { file = "/net/cci-nas-00/data/ceres_data/9e96_47775/08_2025/9e96_47775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e96_47775/08_2025/9e96_47775.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 21500 2.51 5 N 5864 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33952 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "F" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "G" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "H" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "I" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "J" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "K" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "M" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "N" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "O" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "P" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "Q" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "R" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Time building chain proxies: 7.49, per 1000 atoms: 0.22 Number of scatterers: 33952 At special positions: 0 Unit cell: (163.17, 169.83, 198.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 6392 8.00 N 5864 7.00 C 21500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.02 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.04 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 124 " distance=2.02 Simple disulfide: pdb=" SG CYS G 91 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 226 " distance=2.04 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 85 " - pdb=" SG CYS H 91 " distance=2.02 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.02 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.04 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 124 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.02 Simple disulfide: pdb=" SG CYS L 85 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS N 49 " - pdb=" SG CYS N 114 " distance=2.03 Simple disulfide: pdb=" SG CYS N 62 " - pdb=" SG CYS N 94 " distance=2.03 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 259 " - pdb=" SG CYS N 271 " distance=2.03 Simple disulfide: pdb=" SG CYS N 301 " - pdb=" SG CYS N 376 " distance=2.02 Simple disulfide: pdb=" SG CYS N 306 " - pdb=" SG CYS N 380 " distance=2.03 Simple disulfide: pdb=" SG CYS N 328 " - pdb=" SG CYS N 370 " distance=2.03 Simple disulfide: pdb=" SG CYS O 16 " - pdb=" SG CYS O 124 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 25 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 105 " distance=2.02 Simple disulfide: pdb=" SG CYS O 152 " - pdb=" SG CYS O 266 " distance=2.03 Simple disulfide: pdb=" SG CYS O 201 " - pdb=" SG CYS O 226 " distance=2.03 Simple disulfide: pdb=" SG CYS O 203 " - pdb=" SG CYS O 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 85 " - pdb=" SG CYS P 91 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 85 " - pdb=" SG CYS Q 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8136 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 98 sheets defined 13.8% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 398 through 402 removed outlier: 4.084A pdb=" N VAL A 402 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.741A pdb=" N ALA A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.697A pdb=" N ILE B 357 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 402 removed outlier: 3.989A pdb=" N LYS B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 3.793A pdb=" N LEU B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'F' and resid 112 through 116 removed outlier: 4.116A pdb=" N THR F 115 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.873A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'F' and resid 403 through 439 removed outlier: 3.518A pdb=" N ALA F 417 " --> pdb=" O LEU F 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 81 No H-bonds generated for 'chain 'G' and resid 79 through 81' Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 363 through 402 Proline residue: G 399 - end of helix Processing helix chain 'G' and resid 410 through 417 Processing helix chain 'H' and resid 37 through 41 Processing helix chain 'H' and resid 46 through 51 removed outlier: 4.501A pdb=" N ALA H 50 " --> pdb=" O THR H 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'I' and resid 155 through 157 No H-bonds generated for 'chain 'I' and resid 155 through 157' Processing helix chain 'I' and resid 166 through 171 removed outlier: 3.559A pdb=" N LYS I 169 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER I 170 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 116 removed outlier: 3.921A pdb=" N THR J 115 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 254 Processing helix chain 'J' and resid 403 through 438 removed outlier: 3.757A pdb=" N ALA J 417 " --> pdb=" O LEU J 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 363 through 402 Proline residue: K 399 - end of helix Processing helix chain 'K' and resid 409 through 418 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 44 through 48 removed outlier: 3.667A pdb=" N LEU L 48 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 60 Processing helix chain 'M' and resid 143 through 149 Processing helix chain 'M' and resid 165 through 170 removed outlier: 4.257A pdb=" N SER M 170 " --> pdb=" O GLN M 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 116 removed outlier: 3.804A pdb=" N THR N 115 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 246 Processing helix chain 'N' and resid 250 through 254 Processing helix chain 'N' and resid 255 through 259 removed outlier: 3.915A pdb=" N GLY N 258 " --> pdb=" O ALA N 255 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS N 259 " --> pdb=" O PRO N 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 255 through 259' Processing helix chain 'N' and resid 403 through 438 removed outlier: 4.412A pdb=" N ALA N 417 " --> pdb=" O LEU N 413 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER N 418 " --> pdb=" O PHE N 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 224 No H-bonds generated for 'chain 'O' and resid 222 through 224' Processing helix chain 'O' and resid 351 through 363 removed outlier: 3.915A pdb=" N ILE O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 402 Proline residue: O 399 - end of helix removed outlier: 4.001A pdb=" N LEU O 402 " --> pdb=" O THR O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 418 removed outlier: 3.782A pdb=" N ILE O 418 " --> pdb=" O VAL O 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 42 Processing helix chain 'P' and resid 46 through 51 removed outlier: 4.527A pdb=" N ALA P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG P 60 " --> pdb=" O PRO P 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 60' Processing helix chain 'Q' and resid 37 through 41 Processing helix chain 'Q' and resid 44 through 48 Processing helix chain 'R' and resid 143 through 148 removed outlier: 3.797A pdb=" N ALA R 148 " --> pdb=" O GLU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 157 No H-bonds generated for 'chain 'R' and resid 155 through 157' Processing helix chain 'R' and resid 165 through 170 removed outlier: 4.159A pdb=" N SER R 170 " --> pdb=" O GLN R 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.750A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 5.316A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.714A pdb=" N LEU A 129 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.869A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.567A pdb=" N VAL A 108 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP A 75 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 306 removed outlier: 5.533A pdb=" N SER A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.546A pdb=" N CYS A 328 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.572A pdb=" N LEU B 285 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE B 319 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 287 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ARG B 317 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA B 289 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 315 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG B 291 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY B 313 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.908A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N ILE B 45 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N GLN B 104 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N VAL B 47 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU B 102 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA B 49 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE B 100 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 67 Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.942A pdb=" N ASP B 109 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 155 Processing sheet with id=AB8, first strand: chain 'B' and resid 237 through 238 removed outlier: 3.731A pdb=" N GLY B 164 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.514A pdb=" N PHE E 112 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR E 123 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE E 114 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR E 123 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 248 through 251 removed outlier: 4.913A pdb=" N PHE E 198 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ALA E 190 " --> pdb=" O PRO E 201 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 223 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 248 through 251 removed outlier: 6.312A pdb=" N VAL E 240 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 225 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TRP E 242 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA E 223 " --> pdb=" O TRP E 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 2 through 8 removed outlier: 4.422A pdb=" N LYS F 160 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 14 through 19 removed outlier: 5.269A pdb=" N ILE F 31 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 14 through 19 Processing sheet with id=AC8, first strand: chain 'F' and resid 42 through 48 removed outlier: 6.745A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 119 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.742A pdb=" N GLN F 59 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 51 through 54 removed outlier: 5.472A pdb=" N VAL F 108 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP F 75 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AD3, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'F' and resid 296 through 303 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 7.028A pdb=" N CYS F 306 " --> pdb=" O LYS F 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD7, first strand: chain 'F' and resid 387 through 388 removed outlier: 7.457A pdb=" N LEU G 285 " --> pdb=" O PHE G 319 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE G 319 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU G 287 " --> pdb=" O ARG G 317 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG G 317 " --> pdb=" O LEU G 287 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA G 289 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR G 315 " --> pdb=" O ALA G 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG G 291 " --> pdb=" O GLY G 313 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLY G 313 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 14 through 16 Processing sheet with id=AD9, first strand: chain 'G' and resid 31 through 35 removed outlier: 6.837A pdb=" N GLN G 46 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL G 34 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG G 44 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 12.276A pdb=" N SER G 48 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N PHE G 64 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 12.174A pdb=" N GLN G 50 " --> pdb=" O THR G 62 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N THR G 62 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY G 52 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 31 through 35 removed outlier: 6.837A pdb=" N GLN G 46 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL G 34 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG G 44 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N ILE G 45 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N GLN G 104 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N VAL G 47 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N LEU G 102 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ALA G 49 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE G 100 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR G 53 " --> pdb=" O HIS G 96 " (cutoff:3.500A) removed outlier: 12.380A pdb=" N HIS G 96 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 83 through 86 removed outlier: 3.715A pdb=" N SER G 110 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS G 128 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR G 112 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL G 126 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER G 114 " --> pdb=" O CYS G 124 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 148 through 155 Processing sheet with id=AE4, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AE5, first strand: chain 'G' and resid 180 through 183 Processing sheet with id=AE6, first strand: chain 'G' and resid 206 through 211 Processing sheet with id=AE7, first strand: chain 'H' and resid 20 through 25 removed outlier: 6.582A pdb=" N LEU H 20 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU H 111 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR H 22 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU H 113 " --> pdb=" O TYR H 22 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL H 24 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 54 " --> pdb=" O PHE H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.884A pdb=" N LEU H 73 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 72 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 140 through 141 removed outlier: 5.934A pdb=" N PHE I 112 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR I 123 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE I 114 " --> pdb=" O ASN I 121 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N TYR I 123 " --> pdb=" O PRO I 134 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 249 through 251 removed outlier: 4.849A pdb=" N PHE I 198 " --> pdb=" O LEU I 237 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ALA I 190 " --> pdb=" O PRO I 201 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA I 223 " --> pdb=" O ILE I 214 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 249 through 251 removed outlier: 6.837A pdb=" N VAL I 240 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL I 225 " --> pdb=" O VAL I 240 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 2 through 8 removed outlier: 4.180A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 14 through 19 removed outlier: 5.204A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU J 129 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 14 through 19 Processing sheet with id=AF6, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.223A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.919A pdb=" N GLN J 59 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 51 through 54 removed outlier: 5.518A pdb=" N VAL J 108 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP J 75 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AG1, first strand: chain 'J' and resid 219 through 221 Processing sheet with id=AG2, first strand: chain 'J' and resid 298 through 306 removed outlier: 3.596A pdb=" N GLU J 298 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 330 through 332 Processing sheet with id=AG4, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.953A pdb=" N ARG K 291 " --> pdb=" O GLY K 313 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY K 313 " --> pdb=" O ARG K 291 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 18 through 19 removed outlier: 3.992A pdb=" N TYR K 18 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N CYS K 124 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER K 114 " --> pdb=" O CYS K 124 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL K 126 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR K 112 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS K 128 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER K 110 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 31 through 35 removed outlier: 5.588A pdb=" N GLN K 46 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL K 34 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG K 44 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N SER K 48 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET K 67 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY K 52 " --> pdb=" O LYS K 63 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LYS K 63 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 31 through 35 removed outlier: 5.588A pdb=" N GLN K 46 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL K 34 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG K 44 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR K 99 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ALA K 49 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS K 97 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N PHE K 51 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N GLY K 95 " --> pdb=" O PHE K 51 " (cutoff:3.500A) removed outlier: 15.668A pdb=" N TYR K 53 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 17.667A pdb=" N ARG K 93 " --> pdb=" O TYR K 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 149 through 155 Processing sheet with id=AG9, first strand: chain 'K' and resid 237 through 238 removed outlier: 3.561A pdb=" N LEU K 255 " --> pdb=" O ILE K 166 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 180 through 183 Processing sheet with id=AH2, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AH3, first strand: chain 'K' and resid 206 through 207 removed outlier: 3.507A pdb=" N GLU K 200 " --> pdb=" O ILE K 227 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 275 through 279 removed outlier: 3.576A pdb=" N THR K 275 " --> pdb=" O HIS K 286 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG K 317 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 20 through 25 removed outlier: 6.319A pdb=" N LEU L 20 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU L 111 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR L 22 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU L 113 " --> pdb=" O TYR L 22 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL L 24 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN L 54 " --> pdb=" O PHE L 98 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 33 through 36 removed outlier: 6.552A pdb=" N PHE L 33 " --> pdb=" O VAL L 75 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL L 75 " --> pdb=" O PHE L 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY L 35 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR L 74 " --> pdb=" O ASP L 65 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP L 65 " --> pdb=" O TYR L 74 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 111 through 116 removed outlier: 6.337A pdb=" N LEU M 116 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL M 120 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR M 123 " --> pdb=" O PRO M 134 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 182 through 186 removed outlier: 9.144A pdb=" N ALA M 190 " --> pdb=" O PRO M 201 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE M 198 " --> pdb=" O LEU M 237 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL M 240 " --> pdb=" O VAL M 225 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL M 225 " --> pdb=" O VAL M 240 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP M 242 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA M 223 " --> pdb=" O TRP M 242 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 213 through 215 removed outlier: 3.931A pdb=" N ALA M 223 " --> pdb=" O ILE M 214 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA M 223 " --> pdb=" O TRP M 242 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP M 242 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL M 225 " --> pdb=" O VAL M 240 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL M 240 " --> pdb=" O VAL M 225 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 2 through 8 removed outlier: 4.072A pdb=" N LYS N 160 " --> pdb=" O ASP N 281 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 15 through 19 removed outlier: 4.988A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 140 through 147 removed outlier: 6.794A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 51 through 54 removed outlier: 3.732A pdb=" N GLN N 59 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 51 through 54 Processing sheet with id=AI6, first strand: chain 'N' and resid 203 through 204 Processing sheet with id=AI7, first strand: chain 'N' and resid 219 through 221 Processing sheet with id=AI8, first strand: chain 'N' and resid 296 through 303 removed outlier: 3.611A pdb=" N GLU N 298 " --> pdb=" O LYS N 321 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 330 through 332 Processing sheet with id=AJ1, first strand: chain 'N' and resid 387 through 388 Processing sheet with id=AJ2, first strand: chain 'N' and resid 387 through 388 removed outlier: 7.269A pdb=" N LEU O 285 " --> pdb=" O PHE O 319 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE O 319 " --> pdb=" O LEU O 285 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU O 287 " --> pdb=" O ARG O 317 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ARG O 317 " --> pdb=" O LEU O 287 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA O 289 " --> pdb=" O THR O 315 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR O 315 " --> pdb=" O ALA O 289 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG O 291 " --> pdb=" O GLY O 313 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY O 313 " --> pdb=" O ARG O 291 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 14 through 16 Processing sheet with id=AJ4, first strand: chain 'O' and resid 18 through 19 removed outlier: 4.368A pdb=" N TYR O 18 " --> pdb=" O THR O 125 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER O 117 " --> pdb=" O SER O 120 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP O 109 " --> pdb=" O LYS O 128 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 31 through 35 removed outlier: 6.930A pdb=" N GLN O 46 " --> pdb=" O GLU O 32 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL O 34 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG O 44 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR O 99 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ALA O 49 " --> pdb=" O LYS O 97 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LYS O 97 " --> pdb=" O ALA O 49 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N PHE O 51 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N GLY O 95 " --> pdb=" O PHE O 51 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 63 through 67 Processing sheet with id=AJ7, first strand: chain 'O' and resid 147 through 155 Processing sheet with id=AJ8, first strand: chain 'O' and resid 237 through 238 removed outlier: 3.836A pdb=" N ILE O 166 " --> pdb=" O LEU O 255 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 180 through 183 removed outlier: 4.574A pdb=" N VAL O 187 " --> pdb=" O MET O 217 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'O' and resid 206 through 211 Processing sheet with id=AK2, first strand: chain 'P' and resid 20 through 25 removed outlier: 6.529A pdb=" N LEU P 20 " --> pdb=" O GLU P 109 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU P 111 " --> pdb=" O LEU P 20 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR P 22 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU P 113 " --> pdb=" O TYR P 22 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL P 24 " --> pdb=" O LEU P 113 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN P 54 " --> pdb=" O PHE P 98 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P' and resid 33 through 36 removed outlier: 7.150A pdb=" N LEU P 73 " --> pdb=" O VAL P 34 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Q' and resid 20 through 24 removed outlier: 3.536A pdb=" N GLN Q 54 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Q' and resid 33 through 36 removed outlier: 6.521A pdb=" N PHE Q 33 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL Q 75 " --> pdb=" O PHE Q 33 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'R' and resid 140 through 141 removed outlier: 3.901A pdb=" N GLY R 122 " --> pdb=" O ILE R 114 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU R 116 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR R 123 " --> pdb=" O PRO R 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU R 159 " --> pdb=" O ALA R 154 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'R' and resid 249 through 251 removed outlier: 4.892A pdb=" N PHE R 198 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N ALA R 190 " --> pdb=" O PRO R 201 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA R 223 " --> pdb=" O ILE R 214 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'R' and resid 249 through 251 removed outlier: 6.491A pdb=" N VAL R 240 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL R 225 " --> pdb=" O VAL R 240 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10101 1.33 - 1.46: 7706 1.46 - 1.58: 16749 1.58 - 1.71: 0 1.71 - 1.83: 244 Bond restraints: 34800 Sorted by residual: bond pdb=" N TYR F 85 " pdb=" CA TYR F 85 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.10e-03 1.98e+04 1.69e+01 bond pdb=" N VAL R 239 " pdb=" CA VAL R 239 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.03e+01 bond pdb=" N VAL N 177 " pdb=" CA VAL N 177 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N ASP G 70 " pdb=" CA ASP G 70 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N VAL P 24 " pdb=" CA VAL P 24 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.85e+00 ... (remaining 34795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 43888 1.66 - 3.32: 3056 3.32 - 4.98: 369 4.98 - 6.64: 51 6.64 - 8.30: 16 Bond angle restraints: 47380 Sorted by residual: angle pdb=" N ASP G 72 " pdb=" CA ASP G 72 " pdb=" C ASP G 72 " ideal model delta sigma weight residual 113.28 106.18 7.10 1.22e+00 6.72e-01 3.39e+01 angle pdb=" CB HIS F 230 " pdb=" CG HIS F 230 " pdb=" CD2 HIS F 230 " ideal model delta sigma weight residual 131.20 124.56 6.64 1.30e+00 5.92e-01 2.61e+01 angle pdb=" CB HIS L 94 " pdb=" CG HIS L 94 " pdb=" CD2 HIS L 94 " ideal model delta sigma weight residual 131.20 125.14 6.06 1.30e+00 5.92e-01 2.17e+01 angle pdb=" C GLN G 50 " pdb=" N PHE G 51 " pdb=" CA PHE G 51 " ideal model delta sigma weight residual 121.39 129.01 -7.62 1.66e+00 3.63e-01 2.11e+01 angle pdb=" OE1 GLN L 19 " pdb=" CD GLN L 19 " pdb=" NE2 GLN L 19 " ideal model delta sigma weight residual 122.60 118.34 4.26 1.00e+00 1.00e+00 1.82e+01 ... (remaining 47375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18728 17.92 - 35.84: 1675 35.84 - 53.76: 348 53.76 - 71.68: 113 71.68 - 89.60: 28 Dihedral angle restraints: 20892 sinusoidal: 8196 harmonic: 12696 Sorted by residual: dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -145.11 59.11 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CA ARG Q 81 " pdb=" C ARG Q 81 " pdb=" N GLU Q 82 " pdb=" CA GLU Q 82 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA THR G 234 " pdb=" C THR G 234 " pdb=" N LYS G 235 " pdb=" CA LYS G 235 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 20889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4046 0.057 - 0.115: 1077 0.115 - 0.172: 192 0.172 - 0.230: 22 0.230 - 0.287: 3 Chirality restraints: 5340 Sorted by residual: chirality pdb=" CA SER G 22 " pdb=" N SER G 22 " pdb=" C SER G 22 " pdb=" CB SER G 22 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA PRO G 241 " pdb=" N PRO G 241 " pdb=" C PRO G 241 " pdb=" CB PRO G 241 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB THR G 125 " pdb=" CA THR G 125 " pdb=" OG1 THR G 125 " pdb=" CG2 THR G 125 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 5337 not shown) Planarity restraints: 6104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 99 " -0.112 2.00e-02 2.50e+03 5.65e-02 6.39e+01 pdb=" CG TYR G 99 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR G 99 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR G 99 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR G 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR G 99 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR G 99 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR G 99 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 176 " -0.085 2.00e-02 2.50e+03 4.46e-02 3.98e+01 pdb=" CG TYR G 176 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR G 176 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR G 176 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR G 176 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR G 176 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR G 176 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR G 176 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 230 " -0.055 2.00e-02 2.50e+03 4.13e-02 2.56e+01 pdb=" CG HIS F 230 " 0.067 2.00e-02 2.50e+03 pdb=" ND1 HIS F 230 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS F 230 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS F 230 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS F 230 " -0.032 2.00e-02 2.50e+03 ... (remaining 6101 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3589 2.74 - 3.28: 33818 3.28 - 3.82: 56096 3.82 - 4.36: 64070 4.36 - 4.90: 111169 Nonbonded interactions: 268742 Sorted by model distance: nonbonded pdb=" OG1 THR G 297 " pdb=" OG1 THR G 307 " model vdw 2.200 3.040 nonbonded pdb=" OE1 GLU G 186 " pdb=" OH TYR G 188 " model vdw 2.205 3.040 nonbonded pdb=" O GLU N 292 " pdb=" NH1 ARG N 324 " model vdw 2.210 3.120 nonbonded pdb=" O PRO R 180 " pdb=" OH TYR R 184 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR Q 22 " pdb=" OD2 ASP Q 40 " model vdw 2.215 3.040 ... (remaining 268737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.000 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 34852 Z= 0.397 Angle : 0.903 8.295 47484 Z= 0.537 Chirality : 0.053 0.287 5340 Planarity : 0.010 0.126 6104 Dihedral : 14.953 89.599 12600 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 1.20 % Allowed : 13.56 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.13), residues: 4368 helix: 1.22 (0.24), residues: 502 sheet: -0.29 (0.14), residues: 1384 loop : -0.72 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG J 21 TYR 0.112 0.006 TYR G 99 PHE 0.056 0.003 PHE G 51 TRP 0.059 0.004 TRP G 35 HIS 0.012 0.002 HIS G 21 Details of bonding type rmsd covalent geometry : bond 0.00758 (34800) covalent geometry : angle 0.90187 (47380) SS BOND : bond 0.00522 ( 52) SS BOND : angle 1.45542 ( 104) hydrogen bonds : bond 0.21286 ( 1213) hydrogen bonds : angle 7.83154 ( 3426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 1354 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8709 (pt0) cc_final: 0.8228 (pt0) REVERT: A 88 MET cc_start: 0.8565 (mtp) cc_final: 0.8127 (mtp) REVERT: A 93 GLN cc_start: 0.8651 (mm110) cc_final: 0.8146 (mm110) REVERT: A 98 SER cc_start: 0.9155 (t) cc_final: 0.8254 (p) REVERT: A 171 SER cc_start: 0.9217 (m) cc_final: 0.8905 (p) REVERT: A 207 SER cc_start: 0.8908 (m) cc_final: 0.8488 (p) REVERT: A 212 ASP cc_start: 0.9017 (p0) cc_final: 0.8712 (p0) REVERT: A 218 ASP cc_start: 0.8498 (t0) cc_final: 0.8170 (t0) REVERT: A 238 SER cc_start: 0.9284 (t) cc_final: 0.8287 (p) REVERT: A 242 MET cc_start: 0.9453 (mmm) cc_final: 0.8787 (mmm) REVERT: A 260 LYS cc_start: 0.8669 (tttm) cc_final: 0.8067 (tttm) REVERT: A 261 ILE cc_start: 0.9377 (mm) cc_final: 0.9044 (tp) REVERT: A 271 CYS cc_start: 0.8956 (t) cc_final: 0.8534 (m) REVERT: A 293 SER cc_start: 0.9308 (t) cc_final: 0.9018 (p) REVERT: A 340 LYS cc_start: 0.9290 (tttt) cc_final: 0.9046 (ttpp) REVERT: A 341 GLU cc_start: 0.8437 (mp0) cc_final: 0.7507 (mp0) REVERT: A 394 VAL cc_start: 0.9100 (t) cc_final: 0.8825 (p) REVERT: A 399 GLN cc_start: 0.8736 (tp40) cc_final: 0.8393 (mp10) REVERT: A 403 SER cc_start: 0.9307 (p) cc_final: 0.9089 (p) REVERT: A 433 MET cc_start: 0.7630 (mmp) cc_final: 0.7282 (tpt) REVERT: B 80 MET cc_start: 0.7302 (mmt) cc_final: 0.6095 (mmt) REVERT: B 104 GLN cc_start: 0.8104 (tt0) cc_final: 0.7848 (tm-30) REVERT: B 142 PHE cc_start: 0.8355 (m-80) cc_final: 0.8104 (m-80) REVERT: B 156 ASP cc_start: 0.8522 (t0) cc_final: 0.8011 (t70) REVERT: B 168 MET cc_start: 0.8553 (ptp) cc_final: 0.8317 (mtp) REVERT: B 305 ASP cc_start: 0.9046 (m-30) cc_final: 0.8703 (m-30) REVERT: B 330 TRP cc_start: 0.9356 (t-100) cc_final: 0.8709 (t-100) REVERT: B 347 ASP cc_start: 0.8558 (t70) cc_final: 0.8326 (t70) REVERT: B 393 ARG cc_start: 0.7935 (tmm160) cc_final: 0.7731 (ttp80) REVERT: B 394 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7707 (mtt90) REVERT: E 156 MET cc_start: 0.8548 (ppp) cc_final: 0.7880 (ppp) REVERT: E 216 ASP cc_start: 0.8287 (t0) cc_final: 0.7853 (t70) REVERT: E 250 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8442 (ttpp) REVERT: F 195 MET cc_start: 0.8884 (mpp) cc_final: 0.8497 (mpp) REVERT: F 218 ASP cc_start: 0.8756 (t0) cc_final: 0.8090 (t0) REVERT: F 262 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7741 (mp0) REVERT: F 305 ASP cc_start: 0.9330 (t0) cc_final: 0.9116 (t0) REVERT: F 311 ASP cc_start: 0.7815 (p0) cc_final: 0.7586 (p0) REVERT: F 320 TYR cc_start: 0.8050 (p90) cc_final: 0.7579 (p90) REVERT: F 339 LEU cc_start: 0.9313 (mp) cc_final: 0.8991 (mp) REVERT: F 341 GLU cc_start: 0.7569 (mp0) cc_final: 0.7180 (mp0) REVERT: F 367 VAL cc_start: 0.8952 (t) cc_final: 0.8139 (m) REVERT: F 374 THR cc_start: 0.7944 (m) cc_final: 0.7164 (p) REVERT: F 394 VAL cc_start: 0.9036 (t) cc_final: 0.8598 (p) REVERT: F 433 MET cc_start: 0.7411 (mmt) cc_final: 0.6911 (tpp) REVERT: G 21 HIS cc_start: 0.8787 (m90) cc_final: 0.8545 (m-70) REVERT: G 67 MET cc_start: 0.8550 (tpp) cc_final: 0.8320 (tpt) REVERT: G 76 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8716 (mmtp) REVERT: G 125 THR cc_start: 0.9073 (m) cc_final: 0.8705 (p) REVERT: G 191 PRO cc_start: 0.8430 (Cg_exo) cc_final: 0.8178 (Cg_endo) REVERT: G 347 ASP cc_start: 0.8071 (t0) cc_final: 0.7849 (t0) REVERT: G 360 TYR cc_start: 0.8770 (t80) cc_final: 0.8207 (t80) REVERT: H 20 LEU cc_start: 0.8417 (mt) cc_final: 0.7732 (tt) REVERT: H 36 ASN cc_start: 0.6731 (t0) cc_final: 0.6394 (t0) REVERT: H 104 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7247 (mt-10) REVERT: I 130 ARG cc_start: 0.8607 (ptp-110) cc_final: 0.8352 (ptt-90) REVERT: I 193 TYR cc_start: 0.8210 (t80) cc_final: 0.7648 (t80) REVERT: I 222 VAL cc_start: 0.8968 (t) cc_final: 0.8628 (m) REVERT: I 243 ASN cc_start: 0.8530 (t0) cc_final: 0.8187 (m-40) REVERT: I 249 ILE cc_start: 0.7720 (mt) cc_final: 0.7364 (mt) REVERT: J 2 GLU cc_start: 0.8887 (tt0) cc_final: 0.8667 (tp30) REVERT: J 3 HIS cc_start: 0.7424 (t70) cc_final: 0.6789 (t-170) REVERT: J 13 ILE cc_start: 0.9171 (mm) cc_final: 0.8931 (tp) REVERT: J 15 TYR cc_start: 0.8766 (t80) cc_final: 0.8228 (t80) REVERT: J 20 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8449 (pm20) REVERT: J 31 ILE cc_start: 0.8867 (mt) cc_final: 0.8244 (mt) REVERT: J 37 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8472 (mm-30) REVERT: J 43 ASN cc_start: 0.8735 (p0) cc_final: 0.8308 (p0) REVERT: J 45 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8763 (mm-30) REVERT: J 66 LEU cc_start: 0.8017 (mt) cc_final: 0.7729 (mp) REVERT: J 75 ASP cc_start: 0.8461 (t0) cc_final: 0.8001 (t0) REVERT: J 101 THR cc_start: 0.8188 (m) cc_final: 0.7758 (m) REVERT: J 174 ASP cc_start: 0.8564 (m-30) cc_final: 0.8189 (m-30) REVERT: J 251 LEU cc_start: 0.8947 (tp) cc_final: 0.8589 (tp) REVERT: J 257 PHE cc_start: 0.9121 (m-80) cc_final: 0.8883 (m-10) REVERT: J 262 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8114 (mm-30) REVERT: J 279 SER cc_start: 0.9122 (t) cc_final: 0.8638 (m) REVERT: J 280 ILE cc_start: 0.8245 (mp) cc_final: 0.7882 (mm) REVERT: J 292 GLU cc_start: 0.9454 (tp30) cc_final: 0.9204 (mp0) REVERT: J 366 ILE cc_start: 0.9199 (mt) cc_final: 0.8668 (tp) REVERT: J 373 LYS cc_start: 0.9285 (mttm) cc_final: 0.8881 (mttm) REVERT: J 407 TRP cc_start: 0.8067 (m100) cc_final: 0.7753 (m100) REVERT: J 409 TRP cc_start: 0.7686 (m100) cc_final: 0.7480 (m100) REVERT: K 78 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7328 (t0) REVERT: K 96 HIS cc_start: 0.7611 (p90) cc_final: 0.7191 (p90) REVERT: K 141 LEU cc_start: 0.9548 (tp) cc_final: 0.8963 (tt) REVERT: K 156 ASP cc_start: 0.8803 (t0) cc_final: 0.7949 (t0) REVERT: K 158 LEU cc_start: 0.8795 (mt) cc_final: 0.8270 (mt) REVERT: K 225 GLN cc_start: 0.8587 (mt0) cc_final: 0.8159 (mt0) REVERT: K 235 LYS cc_start: 0.6696 (tmtp) cc_final: 0.5874 (mmmt) REVERT: K 360 TYR cc_start: 0.8951 (t80) cc_final: 0.8637 (t80) REVERT: L 56 VAL cc_start: 0.9366 (t) cc_final: 0.8667 (m) REVERT: L 58 ASN cc_start: 0.8666 (p0) cc_final: 0.8458 (t0) REVERT: L 92 VAL cc_start: 0.8449 (t) cc_final: 0.7901 (t) REVERT: L 105 LEU cc_start: 0.9086 (tp) cc_final: 0.8054 (tp) REVERT: L 106 PHE cc_start: 0.7815 (m-80) cc_final: 0.7027 (m-80) REVERT: L 109 GLU cc_start: 0.8601 (tt0) cc_final: 0.8096 (pm20) REVERT: L 111 GLU cc_start: 0.8643 (tt0) cc_final: 0.8314 (tp30) REVERT: L 113 LEU cc_start: 0.8572 (mt) cc_final: 0.8265 (mp) REVERT: M 110 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7523 (mtpp) REVERT: M 125 CYS cc_start: 0.7742 (t) cc_final: 0.7421 (t) REVERT: M 176 THR cc_start: 0.7985 (t) cc_final: 0.6761 (m) REVERT: M 183 PHE cc_start: 0.7992 (m-80) cc_final: 0.7684 (m-10) REVERT: N 15 TYR cc_start: 0.8869 (t80) cc_final: 0.8393 (t80) REVERT: N 31 ILE cc_start: 0.8755 (mt) cc_final: 0.8039 (mt) REVERT: N 75 ASP cc_start: 0.8881 (t0) cc_final: 0.8507 (t0) REVERT: N 88 MET cc_start: 0.7976 (mmt) cc_final: 0.6769 (mmt) REVERT: N 93 GLN cc_start: 0.8798 (tp40) cc_final: 0.8267 (tp40) REVERT: N 117 ASP cc_start: 0.8957 (t0) cc_final: 0.8630 (t0) REVERT: N 125 HIS cc_start: 0.7754 (m90) cc_final: 0.7093 (m90) REVERT: N 162 ILE cc_start: 0.9122 (mp) cc_final: 0.8692 (tp) REVERT: N 213 ILE cc_start: 0.8878 (mt) cc_final: 0.8572 (mp) REVERT: N 218 ASP cc_start: 0.8721 (t70) cc_final: 0.8488 (t0) REVERT: N 264 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8650 (tm-30) REVERT: N 298 GLU cc_start: 0.8635 (pm20) cc_final: 0.8405 (pm20) REVERT: N 331 HIS cc_start: 0.8519 (t-170) cc_final: 0.7768 (t70) REVERT: N 366 ILE cc_start: 0.9297 (mt) cc_final: 0.9070 (tp) REVERT: N 379 GLU cc_start: 0.8046 (tp30) cc_final: 0.7835 (tp30) REVERT: N 387 ILE cc_start: 0.9169 (mm) cc_final: 0.8827 (mm) REVERT: N 396 GLN cc_start: 0.9332 (tt0) cc_final: 0.8752 (tt0) REVERT: N 399 GLN cc_start: 0.7582 (mp10) cc_final: 0.7372 (mp10) REVERT: N 411 LEU cc_start: 0.8844 (mt) cc_final: 0.8554 (tt) REVERT: O 34 VAL cc_start: 0.9577 (t) cc_final: 0.9305 (m) REVERT: O 36 ASP cc_start: 0.9164 (p0) cc_final: 0.8942 (p0) REVERT: O 67 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7987 (tpp) REVERT: O 80 MET cc_start: 0.9336 (mmp) cc_final: 0.8919 (mmt) REVERT: O 127 GLU cc_start: 0.5784 (mm-30) cc_final: 0.5530 (tm-30) REVERT: O 138 GLU cc_start: 0.8658 (tt0) cc_final: 0.8065 (tt0) REVERT: O 165 TYR cc_start: 0.9007 (p90) cc_final: 0.8539 (p90) REVERT: O 168 MET cc_start: 0.8179 (mmm) cc_final: 0.7716 (tpp) REVERT: O 225 GLN cc_start: 0.7572 (mt0) cc_final: 0.7311 (mt0) REVERT: O 238 PHE cc_start: 0.8921 (t80) cc_final: 0.8705 (t80) REVERT: O 239 ASN cc_start: 0.9146 (t0) cc_final: 0.8921 (t0) REVERT: O 334 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8912 (mm-30) REVERT: O 351 TRP cc_start: 0.8427 (m100) cc_final: 0.7720 (m-90) REVERT: P 80 ASP cc_start: 0.8205 (t0) cc_final: 0.7473 (m-30) REVERT: P 95 LEU cc_start: 0.8187 (tp) cc_final: 0.7956 (tp) REVERT: P 96 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8130 (mp0) REVERT: P 101 ASN cc_start: 0.8746 (m-40) cc_final: 0.7921 (p0) REVERT: Q 26 GLU cc_start: 0.6458 (pt0) cc_final: 0.6150 (pt0) REVERT: Q 55 THR cc_start: 0.8759 (p) cc_final: 0.8555 (t) REVERT: Q 103 LEU cc_start: 0.8776 (mt) cc_final: 0.8367 (mt) REVERT: R 125 CYS cc_start: 0.8463 (t) cc_final: 0.7398 (t) REVERT: R 127 VAL cc_start: 0.8976 (t) cc_final: 0.8474 (m) REVERT: R 130 ARG cc_start: 0.8246 (ptp-110) cc_final: 0.7983 (ptp-170) REVERT: R 132 MET cc_start: 0.8710 (mpp) cc_final: 0.8262 (mpp) REVERT: R 193 TYR cc_start: 0.8680 (t80) cc_final: 0.8328 (t80) REVERT: R 209 ASP cc_start: 0.7778 (m-30) cc_final: 0.7357 (t0) REVERT: R 212 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7877 (mtt-85) outliers start: 45 outliers final: 9 residues processed: 1375 average time/residue: 0.2107 time to fit residues: 463.0282 Evaluate side-chains 898 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 887 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 396 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 233 GLN B 249 HIS E 185 ASN E 192 GLN ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN G 252 GLN ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 HIS H 28 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 93 GLN J 235 GLN J 327 HIS ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 HIS ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 GLN L 19 GLN M 119 GLN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN ** N 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 HIS N 396 GLN ** O 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 GLN R 143 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.154562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115860 restraints weight = 73744.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119146 restraints weight = 37499.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121218 restraints weight = 24152.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122324 restraints weight = 18269.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123210 restraints weight = 15865.187| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34852 Z= 0.156 Angle : 0.660 12.197 47484 Z= 0.348 Chirality : 0.046 0.229 5340 Planarity : 0.005 0.057 6104 Dihedral : 5.119 25.410 4744 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.27 % Allowed : 3.72 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.13), residues: 4368 helix: 1.64 (0.24), residues: 510 sheet: -0.16 (0.14), residues: 1357 loop : -0.59 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 134 TYR 0.034 0.002 TYR K 206 PHE 0.033 0.002 PHE L 106 TRP 0.020 0.001 TRP M 186 HIS 0.016 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00356 (34800) covalent geometry : angle 0.65542 (47380) SS BOND : bond 0.00775 ( 52) SS BOND : angle 1.81205 ( 104) hydrogen bonds : bond 0.04154 ( 1213) hydrogen bonds : angle 5.92879 ( 3426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1108 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8606 (mtp) cc_final: 0.7919 (mtp) REVERT: A 93 GLN cc_start: 0.8755 (mm110) cc_final: 0.8480 (mm110) REVERT: A 171 SER cc_start: 0.8783 (m) cc_final: 0.8573 (p) REVERT: A 212 ASP cc_start: 0.8718 (p0) cc_final: 0.8380 (p0) REVERT: A 240 TYR cc_start: 0.9148 (t80) cc_final: 0.8890 (t80) REVERT: A 341 GLU cc_start: 0.8651 (mp0) cc_final: 0.8176 (mp0) REVERT: A 403 SER cc_start: 0.8858 (p) cc_final: 0.8636 (p) REVERT: A 433 MET cc_start: 0.7594 (mmp) cc_final: 0.7186 (tpp) REVERT: B 13 LEU cc_start: 0.7970 (pp) cc_final: 0.7479 (tt) REVERT: B 36 ASP cc_start: 0.8467 (p0) cc_final: 0.8200 (p0) REVERT: B 80 MET cc_start: 0.7282 (mmt) cc_final: 0.6353 (mmt) REVERT: B 121 GLU cc_start: 0.8588 (pm20) cc_final: 0.8072 (pm20) REVERT: B 245 ARG cc_start: 0.8872 (ptp-170) cc_final: 0.8157 (ptp90) REVERT: E 125 CYS cc_start: 0.6793 (m) cc_final: 0.6262 (m) REVERT: E 186 TRP cc_start: 0.8112 (t60) cc_final: 0.7842 (t60) REVERT: E 194 GLU cc_start: 0.8349 (pp20) cc_final: 0.8062 (pp20) REVERT: E 197 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8139 (mtm110) REVERT: E 216 ASP cc_start: 0.8544 (t0) cc_final: 0.7748 (t70) REVERT: F 195 MET cc_start: 0.8852 (mpp) cc_final: 0.8231 (mpp) REVERT: F 218 ASP cc_start: 0.8472 (t0) cc_final: 0.8040 (t0) REVERT: F 246 ASN cc_start: 0.8792 (t0) cc_final: 0.8541 (t0) REVERT: F 262 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7696 (mp0) REVERT: F 280 ILE cc_start: 0.9158 (mm) cc_final: 0.8935 (mm) REVERT: F 320 TYR cc_start: 0.8072 (p90) cc_final: 0.7617 (p90) REVERT: F 340 LYS cc_start: 0.9411 (tttp) cc_final: 0.8963 (ttpp) REVERT: F 365 PHE cc_start: 0.8726 (p90) cc_final: 0.8381 (p90) REVERT: F 367 VAL cc_start: 0.9052 (t) cc_final: 0.8699 (m) REVERT: F 374 THR cc_start: 0.8318 (m) cc_final: 0.7985 (p) REVERT: F 394 VAL cc_start: 0.9247 (t) cc_final: 0.8920 (p) REVERT: F 397 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6957 (tt0) REVERT: G 168 MET cc_start: 0.7523 (mtp) cc_final: 0.7231 (mtm) REVERT: G 347 ASP cc_start: 0.7923 (t0) cc_final: 0.7642 (t0) REVERT: G 360 TYR cc_start: 0.8807 (t80) cc_final: 0.8072 (t80) REVERT: G 367 THR cc_start: 0.8863 (m) cc_final: 0.8589 (p) REVERT: G 393 ARG cc_start: 0.7828 (ttt90) cc_final: 0.7391 (tpp80) REVERT: G 395 ASP cc_start: 0.8511 (m-30) cc_final: 0.8079 (m-30) REVERT: H 20 LEU cc_start: 0.8028 (mt) cc_final: 0.7181 (tt) REVERT: H 63 TYR cc_start: 0.7956 (m-80) cc_final: 0.7643 (m-80) REVERT: H 67 ASN cc_start: 0.8368 (t0) cc_final: 0.8094 (t0) REVERT: H 99 LEU cc_start: 0.8438 (mp) cc_final: 0.8217 (mp) REVERT: I 174 GLN cc_start: 0.8903 (mm110) cc_final: 0.8647 (mm110) REVERT: I 193 TYR cc_start: 0.8141 (t80) cc_final: 0.7700 (t80) REVERT: I 198 PHE cc_start: 0.8768 (m-10) cc_final: 0.8556 (m-10) REVERT: I 243 ASN cc_start: 0.8233 (t0) cc_final: 0.7776 (m-40) REVERT: J 75 ASP cc_start: 0.8133 (t0) cc_final: 0.7686 (t0) REVERT: J 251 LEU cc_start: 0.9189 (tp) cc_final: 0.8805 (tp) REVERT: J 257 PHE cc_start: 0.9010 (m-80) cc_final: 0.8797 (m-10) REVERT: J 262 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8133 (mm-30) REVERT: J 278 ILE cc_start: 0.9544 (tt) cc_final: 0.9293 (mm) REVERT: J 280 ILE cc_start: 0.9308 (mp) cc_final: 0.8646 (mp) REVERT: J 366 ILE cc_start: 0.9330 (mt) cc_final: 0.8983 (tp) REVERT: J 390 GLU cc_start: 0.8448 (tt0) cc_final: 0.7967 (tm-30) REVERT: J 404 LYS cc_start: 0.8888 (mppt) cc_final: 0.8470 (tppt) REVERT: J 407 TRP cc_start: 0.8477 (m100) cc_final: 0.7821 (m100) REVERT: K 54 ASN cc_start: 0.8014 (p0) cc_final: 0.7800 (p0) REVERT: K 96 HIS cc_start: 0.7428 (p90) cc_final: 0.6985 (p90) REVERT: K 141 LEU cc_start: 0.9376 (tp) cc_final: 0.9100 (tt) REVERT: K 156 ASP cc_start: 0.8397 (t0) cc_final: 0.7991 (t0) REVERT: K 225 GLN cc_start: 0.8161 (mt0) cc_final: 0.7781 (mt0) REVERT: K 235 LYS cc_start: 0.5623 (tttm) cc_final: 0.5014 (mmmt) REVERT: K 305 ASP cc_start: 0.8107 (t0) cc_final: 0.7825 (t0) REVERT: K 360 TYR cc_start: 0.9027 (t80) cc_final: 0.8634 (t80) REVERT: L 20 LEU cc_start: 0.7336 (mt) cc_final: 0.7100 (mp) REVERT: L 26 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8555 (tm-30) REVERT: L 77 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8849 (mm-30) REVERT: L 80 ASP cc_start: 0.7968 (t0) cc_final: 0.7516 (t0) REVERT: L 92 VAL cc_start: 0.8607 (t) cc_final: 0.8173 (t) REVERT: L 101 ASN cc_start: 0.8618 (t0) cc_final: 0.7643 (m110) REVERT: L 104 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6504 (tm-30) REVERT: L 105 LEU cc_start: 0.8600 (tp) cc_final: 0.8290 (tp) REVERT: L 108 VAL cc_start: 0.9018 (t) cc_final: 0.8781 (m) REVERT: L 109 GLU cc_start: 0.8493 (tt0) cc_final: 0.8194 (pm20) REVERT: L 111 GLU cc_start: 0.8687 (tt0) cc_final: 0.8456 (tp30) REVERT: M 125 CYS cc_start: 0.7594 (t) cc_final: 0.7341 (t) REVERT: M 135 LEU cc_start: 0.9114 (tp) cc_final: 0.8804 (tp) REVERT: M 149 VAL cc_start: 0.8145 (t) cc_final: 0.7895 (p) REVERT: M 176 THR cc_start: 0.7865 (t) cc_final: 0.6751 (t) REVERT: M 178 ASP cc_start: 0.8093 (p0) cc_final: 0.7665 (p0) REVERT: M 183 PHE cc_start: 0.7959 (m-80) cc_final: 0.7617 (m-10) REVERT: M 194 GLU cc_start: 0.8696 (tt0) cc_final: 0.8464 (pp20) REVERT: M 195 ASN cc_start: 0.8783 (m-40) cc_final: 0.8221 (m-40) REVERT: M 220 ARG cc_start: 0.8711 (mtm180) cc_final: 0.8254 (mtm180) REVERT: N 15 TYR cc_start: 0.9013 (t80) cc_final: 0.8394 (t80) REVERT: N 93 GLN cc_start: 0.8556 (tp40) cc_final: 0.7870 (tp40) REVERT: N 117 ASP cc_start: 0.8928 (t0) cc_final: 0.8492 (t0) REVERT: N 143 ARG cc_start: 0.8316 (ttm110) cc_final: 0.8113 (ttm-80) REVERT: N 144 LEU cc_start: 0.8780 (mt) cc_final: 0.8425 (mt) REVERT: N 174 ASP cc_start: 0.8251 (m-30) cc_final: 0.7674 (p0) REVERT: N 187 TYR cc_start: 0.8890 (t80) cc_final: 0.8632 (t80) REVERT: N 262 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8128 (tt0) REVERT: N 264 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8343 (tm-30) REVERT: N 321 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8616 (mtmm) REVERT: N 396 GLN cc_start: 0.9131 (tt0) cc_final: 0.8589 (tt0) REVERT: N 402 VAL cc_start: 0.9231 (t) cc_final: 0.8845 (p) REVERT: O 34 VAL cc_start: 0.9634 (t) cc_final: 0.9293 (m) REVERT: O 36 ASP cc_start: 0.8965 (p0) cc_final: 0.8671 (p0) REVERT: O 67 MET cc_start: 0.8191 (tpp) cc_final: 0.7892 (tpp) REVERT: O 80 MET cc_start: 0.9084 (mmp) cc_final: 0.8119 (mmm) REVERT: O 121 GLU cc_start: 0.8275 (pp20) cc_final: 0.7303 (pm20) REVERT: O 125 THR cc_start: 0.9298 (m) cc_final: 0.8725 (p) REVERT: O 165 TYR cc_start: 0.8427 (p90) cc_final: 0.8155 (p90) REVERT: O 238 PHE cc_start: 0.9099 (t80) cc_final: 0.8880 (t80) REVERT: O 239 ASN cc_start: 0.9231 (t0) cc_final: 0.8783 (t0) REVERT: O 334 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8343 (mm-30) REVERT: P 95 LEU cc_start: 0.7816 (tp) cc_final: 0.7517 (tp) REVERT: P 101 ASN cc_start: 0.8603 (m-40) cc_final: 0.7765 (p0) REVERT: Q 55 THR cc_start: 0.8696 (p) cc_final: 0.8488 (t) REVERT: Q 99 LEU cc_start: 0.9049 (mt) cc_final: 0.8843 (mt) REVERT: Q 104 GLU cc_start: 0.6626 (mp0) cc_final: 0.6293 (mp0) REVERT: R 115 MET cc_start: 0.8725 (mmm) cc_final: 0.8405 (mmm) REVERT: R 125 CYS cc_start: 0.8815 (t) cc_final: 0.7998 (t) REVERT: R 126 VAL cc_start: 0.9522 (m) cc_final: 0.9314 (m) REVERT: R 127 VAL cc_start: 0.9078 (t) cc_final: 0.8766 (m) REVERT: R 133 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8244 (tttm) REVERT: R 143 ASN cc_start: 0.5745 (m-40) cc_final: 0.5485 (t0) REVERT: R 160 GLU cc_start: 0.8365 (mp0) cc_final: 0.7559 (mp0) REVERT: R 197 ARG cc_start: 0.9270 (ttm-80) cc_final: 0.9003 (ttm-80) REVERT: R 207 LYS cc_start: 0.9234 (tttm) cc_final: 0.8973 (tptp) REVERT: R 209 ASP cc_start: 0.8149 (m-30) cc_final: 0.7520 (t0) REVERT: R 216 ASP cc_start: 0.8291 (p0) cc_final: 0.7817 (p0) outliers start: 10 outliers final: 3 residues processed: 1116 average time/residue: 0.2093 time to fit residues: 377.4070 Evaluate side-chains 838 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 835 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 58 optimal weight: 8.9990 chunk 422 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 185 optimal weight: 30.0000 chunk 11 optimal weight: 0.2980 chunk 332 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN B 174 HIS B 341 GLN E 145 GLN E 188 HIS E 192 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 ASN J 399 GLN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN L 94 HIS M 119 GLN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN ** N 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS O 50 GLN ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 169 HIS P 21 HIS R 143 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101708 restraints weight = 76764.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105809 restraints weight = 38721.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107289 restraints weight = 21034.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107592 restraints weight = 16759.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107590 restraints weight = 16664.267| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 34852 Z= 0.219 Angle : 0.659 10.286 47484 Z= 0.346 Chirality : 0.046 0.226 5340 Planarity : 0.005 0.057 6104 Dihedral : 5.062 24.589 4744 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.13), residues: 4368 helix: 1.71 (0.24), residues: 506 sheet: -0.14 (0.14), residues: 1365 loop : -0.59 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 220 TYR 0.026 0.002 TYR I 157 PHE 0.023 0.002 PHE J 87 TRP 0.020 0.002 TRP M 186 HIS 0.022 0.001 HIS G 349 Details of bonding type rmsd covalent geometry : bond 0.00493 (34800) covalent geometry : angle 0.65546 (47380) SS BOND : bond 0.00566 ( 52) SS BOND : angle 1.61777 ( 104) hydrogen bonds : bond 0.03960 ( 1213) hydrogen bonds : angle 5.62671 ( 3426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 966 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8753 (p0) cc_final: 0.8406 (p0) REVERT: A 240 TYR cc_start: 0.9311 (t80) cc_final: 0.8916 (t80) REVERT: A 321 LYS cc_start: 0.9651 (mtpt) cc_final: 0.9354 (mtpp) REVERT: A 390 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8351 (pt0) REVERT: A 433 MET cc_start: 0.7661 (mmp) cc_final: 0.7294 (tpp) REVERT: B 80 MET cc_start: 0.7425 (mmt) cc_final: 0.6489 (mmt) REVERT: E 125 CYS cc_start: 0.6923 (m) cc_final: 0.6498 (m) REVERT: E 140 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8266 (tptt) REVERT: E 141 ILE cc_start: 0.8400 (tp) cc_final: 0.8075 (tp) REVERT: E 186 TRP cc_start: 0.8519 (t60) cc_final: 0.7911 (t60) REVERT: E 194 GLU cc_start: 0.8461 (pp20) cc_final: 0.7985 (pp20) REVERT: E 197 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8047 (mtm110) REVERT: E 216 ASP cc_start: 0.8421 (t0) cc_final: 0.7967 (t70) REVERT: E 220 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7472 (mtm-85) REVERT: E 250 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8011 (mtpt) REVERT: F 99 GLU cc_start: 0.7722 (tp30) cc_final: 0.7509 (tp30) REVERT: F 195 MET cc_start: 0.8977 (mpp) cc_final: 0.8309 (mpp) REVERT: F 218 ASP cc_start: 0.8534 (t0) cc_final: 0.8174 (t0) REVERT: F 246 ASN cc_start: 0.9022 (t0) cc_final: 0.8663 (t0) REVERT: F 308 TYR cc_start: 0.8653 (p90) cc_final: 0.8449 (p90) REVERT: F 320 TYR cc_start: 0.8137 (p90) cc_final: 0.7680 (p90) REVERT: F 340 LYS cc_start: 0.9376 (tttp) cc_final: 0.8909 (ttpp) REVERT: F 367 VAL cc_start: 0.9012 (t) cc_final: 0.8601 (m) REVERT: F 374 THR cc_start: 0.7830 (m) cc_final: 0.7404 (p) REVERT: F 394 VAL cc_start: 0.9378 (t) cc_final: 0.9013 (p) REVERT: F 397 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6965 (tt0) REVERT: G 168 MET cc_start: 0.7829 (mtp) cc_final: 0.7345 (mtm) REVERT: G 327 GLU cc_start: 0.8008 (tt0) cc_final: 0.7234 (tt0) REVERT: G 347 ASP cc_start: 0.8045 (t0) cc_final: 0.7667 (t0) REVERT: G 360 TYR cc_start: 0.8843 (t80) cc_final: 0.8075 (t80) REVERT: G 367 THR cc_start: 0.9048 (m) cc_final: 0.8778 (p) REVERT: G 393 ARG cc_start: 0.8000 (ttt90) cc_final: 0.7539 (tpp80) REVERT: H 20 LEU cc_start: 0.7974 (mt) cc_final: 0.7187 (tt) REVERT: H 28 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7755 (mm110) REVERT: H 67 ASN cc_start: 0.8457 (t0) cc_final: 0.8211 (t0) REVERT: H 99 LEU cc_start: 0.8721 (mp) cc_final: 0.8404 (mp) REVERT: H 107 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7226 (mm-40) REVERT: H 109 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7147 (mm-30) REVERT: H 111 GLU cc_start: 0.2734 (tp30) cc_final: 0.2384 (tp30) REVERT: I 156 MET cc_start: 0.8766 (ppp) cc_final: 0.8485 (ppp) REVERT: I 193 TYR cc_start: 0.8281 (t80) cc_final: 0.7800 (t80) REVERT: I 198 PHE cc_start: 0.8918 (m-10) cc_final: 0.8675 (m-10) REVERT: I 222 VAL cc_start: 0.8990 (t) cc_final: 0.8707 (m) REVERT: I 243 ASN cc_start: 0.8199 (t0) cc_final: 0.7681 (m-40) REVERT: J 57 SER cc_start: 0.9185 (m) cc_final: 0.8059 (p) REVERT: J 67 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7049 (tm-30) REVERT: J 251 LEU cc_start: 0.9310 (tp) cc_final: 0.8965 (tp) REVERT: J 257 PHE cc_start: 0.9026 (m-80) cc_final: 0.8823 (m-10) REVERT: J 262 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8139 (mp0) REVERT: J 278 ILE cc_start: 0.9593 (tt) cc_final: 0.9350 (mm) REVERT: J 366 ILE cc_start: 0.9381 (mt) cc_final: 0.8989 (tp) REVERT: J 390 GLU cc_start: 0.8635 (tt0) cc_final: 0.7390 (tm-30) REVERT: J 396 GLN cc_start: 0.8169 (pm20) cc_final: 0.7969 (pm20) REVERT: J 404 LYS cc_start: 0.8896 (mppt) cc_final: 0.8572 (tppt) REVERT: K 24 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.7715 (Cg_endo) REVERT: K 46 GLN cc_start: 0.8065 (tt0) cc_final: 0.7456 (tt0) REVERT: K 54 ASN cc_start: 0.8031 (p0) cc_final: 0.7793 (p0) REVERT: K 96 HIS cc_start: 0.7637 (p90) cc_final: 0.7141 (p90) REVERT: K 104 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8489 (tp40) REVERT: K 141 LEU cc_start: 0.9453 (tp) cc_final: 0.9018 (tt) REVERT: K 156 ASP cc_start: 0.8311 (t0) cc_final: 0.7839 (t0) REVERT: K 158 LEU cc_start: 0.9257 (mt) cc_final: 0.8548 (mt) REVERT: K 225 GLN cc_start: 0.8442 (mt0) cc_final: 0.8063 (mt0) REVERT: K 235 LYS cc_start: 0.5369 (tttm) cc_final: 0.4782 (mmmt) REVERT: K 305 ASP cc_start: 0.8434 (t0) cc_final: 0.8127 (t0) REVERT: K 334 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8264 (mp0) REVERT: L 26 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8313 (tm-30) REVERT: L 28 GLN cc_start: 0.7209 (mm110) cc_final: 0.6816 (mm110) REVERT: L 77 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8596 (mm-30) REVERT: L 80 ASP cc_start: 0.7979 (t0) cc_final: 0.7458 (t0) REVERT: L 92 VAL cc_start: 0.8474 (t) cc_final: 0.7925 (t) REVERT: L 101 ASN cc_start: 0.8901 (t0) cc_final: 0.7899 (m110) REVERT: L 104 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6859 (tm-30) REVERT: L 109 GLU cc_start: 0.8502 (tt0) cc_final: 0.8193 (pm20) REVERT: L 111 GLU cc_start: 0.8776 (tt0) cc_final: 0.8511 (tp30) REVERT: M 125 CYS cc_start: 0.7838 (t) cc_final: 0.7505 (t) REVERT: M 176 THR cc_start: 0.7398 (t) cc_final: 0.5475 (t) REVERT: M 178 ASP cc_start: 0.8246 (p0) cc_final: 0.7786 (p0) REVERT: M 195 ASN cc_start: 0.8795 (m-40) cc_final: 0.8505 (m110) REVERT: M 202 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8076 (ttt90) REVERT: M 212 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7929 (mmm-85) REVERT: M 220 ARG cc_start: 0.8641 (mtm180) cc_final: 0.8107 (mtm180) REVERT: N 125 HIS cc_start: 0.7252 (m-70) cc_final: 0.6905 (m90) REVERT: N 144 LEU cc_start: 0.8769 (mt) cc_final: 0.8419 (mt) REVERT: N 187 TYR cc_start: 0.8965 (t80) cc_final: 0.8623 (t80) REVERT: N 262 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8168 (mt-10) REVERT: N 321 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8749 (mtmt) REVERT: N 396 GLN cc_start: 0.9233 (tt0) cc_final: 0.8944 (tt0) REVERT: O 34 VAL cc_start: 0.9672 (t) cc_final: 0.9401 (m) REVERT: O 67 MET cc_start: 0.8341 (tpp) cc_final: 0.7979 (tpp) REVERT: O 80 MET cc_start: 0.9156 (mmp) cc_final: 0.8766 (mmp) REVERT: O 125 THR cc_start: 0.9346 (m) cc_final: 0.8846 (p) REVERT: O 165 TYR cc_start: 0.8577 (p90) cc_final: 0.8241 (p90) REVERT: O 230 LYS cc_start: 0.8817 (pttm) cc_final: 0.8595 (pmtt) REVERT: O 239 ASN cc_start: 0.9259 (t0) cc_final: 0.8950 (t0) REVERT: O 305 ASP cc_start: 0.8863 (m-30) cc_final: 0.8541 (t0) REVERT: P 20 LEU cc_start: 0.8055 (mt) cc_final: 0.7649 (mt) REVERT: P 48 LEU cc_start: 0.9510 (mt) cc_final: 0.9280 (mt) REVERT: P 61 THR cc_start: 0.8511 (p) cc_final: 0.8274 (p) REVERT: P 69 GLU cc_start: 0.9039 (mp0) cc_final: 0.8640 (mp0) REVERT: P 80 ASP cc_start: 0.8064 (m-30) cc_final: 0.7774 (m-30) REVERT: P 96 GLU cc_start: 0.7449 (mp0) cc_final: 0.7109 (mp0) REVERT: Q 29 GLU cc_start: 0.8726 (tp30) cc_final: 0.8463 (mt-10) REVERT: Q 55 THR cc_start: 0.8494 (p) cc_final: 0.8114 (t) REVERT: Q 77 GLU cc_start: 0.8441 (tp30) cc_final: 0.7847 (pt0) REVERT: R 115 MET cc_start: 0.8631 (mmm) cc_final: 0.8286 (mmm) REVERT: R 116 LEU cc_start: 0.9170 (tp) cc_final: 0.8944 (tp) REVERT: R 125 CYS cc_start: 0.8938 (t) cc_final: 0.8157 (t) REVERT: R 126 VAL cc_start: 0.9413 (m) cc_final: 0.9195 (m) REVERT: R 127 VAL cc_start: 0.9153 (t) cc_final: 0.8859 (m) REVERT: R 133 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8357 (tttm) REVERT: R 143 ASN cc_start: 0.6060 (m110) cc_final: 0.5768 (t0) REVERT: R 160 GLU cc_start: 0.8359 (mp0) cc_final: 0.7700 (mp0) REVERT: R 194 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7152 (tm-30) REVERT: R 197 ARG cc_start: 0.9252 (ttm-80) cc_final: 0.9041 (ttm-80) REVERT: R 207 LYS cc_start: 0.9259 (tttm) cc_final: 0.9031 (tptp) REVERT: R 209 ASP cc_start: 0.8200 (m-30) cc_final: 0.7609 (t0) REVERT: R 212 ARG cc_start: 0.8828 (mmt180) cc_final: 0.8203 (mtt-85) REVERT: R 250 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7020 (mttt) outliers start: 3 outliers final: 2 residues processed: 969 average time/residue: 0.2234 time to fit residues: 350.6539 Evaluate side-chains 786 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 784 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 275 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 409 optimal weight: 30.0000 chunk 355 optimal weight: 20.0000 chunk 431 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 288 optimal weight: 0.0980 chunk 146 optimal weight: 10.0000 chunk 413 optimal weight: 6.9990 chunk 326 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 100 ASN A 355 HIS A 396 GLN ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 HIS ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN J 333 HIS J 364 ASN J 399 GLN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 405 ASN M 119 GLN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN ** N 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105773 restraints weight = 76604.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109784 restraints weight = 38504.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111203 restraints weight = 21069.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111565 restraints weight = 16981.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111755 restraints weight = 16298.276| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34852 Z= 0.158 Angle : 0.614 9.903 47484 Z= 0.319 Chirality : 0.045 0.226 5340 Planarity : 0.004 0.059 6104 Dihedral : 4.953 23.879 4744 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.13), residues: 4368 helix: 1.74 (0.23), residues: 506 sheet: -0.18 (0.14), residues: 1391 loop : -0.56 (0.13), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 60 TYR 0.024 0.002 TYR I 157 PHE 0.023 0.002 PHE L 33 TRP 0.026 0.002 TRP M 186 HIS 0.009 0.001 HIS R 188 Details of bonding type rmsd covalent geometry : bond 0.00360 (34800) covalent geometry : angle 0.61041 (47380) SS BOND : bond 0.00372 ( 52) SS BOND : angle 1.48697 ( 104) hydrogen bonds : bond 0.03528 ( 1213) hydrogen bonds : angle 5.41480 ( 3426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 943 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8531 (mtm) cc_final: 0.8218 (mtp) REVERT: A 212 ASP cc_start: 0.8733 (p0) cc_final: 0.8378 (p0) REVERT: A 321 LYS cc_start: 0.9574 (mtpt) cc_final: 0.9347 (mtpp) REVERT: A 433 MET cc_start: 0.7683 (mmp) cc_final: 0.7447 (tpt) REVERT: B 80 MET cc_start: 0.7466 (mmt) cc_final: 0.6651 (mmm) REVERT: B 156 ASP cc_start: 0.7759 (t0) cc_final: 0.7509 (t0) REVERT: B 239 ASN cc_start: 0.8950 (t0) cc_final: 0.8670 (t0) REVERT: E 125 CYS cc_start: 0.7012 (m) cc_final: 0.6497 (m) REVERT: E 140 LYS cc_start: 0.8633 (tmtt) cc_final: 0.8353 (tmtt) REVERT: E 145 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8927 (mp10) REVERT: E 175 TYR cc_start: 0.7234 (p90) cc_final: 0.6773 (p90) REVERT: E 186 TRP cc_start: 0.8411 (t60) cc_final: 0.7851 (t60) REVERT: E 194 GLU cc_start: 0.8587 (pp20) cc_final: 0.7878 (pp20) REVERT: E 197 ARG cc_start: 0.8688 (mtm-85) cc_final: 0.8171 (mtm110) REVERT: E 220 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7472 (mtm-85) REVERT: E 250 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8049 (mtpt) REVERT: F 66 LEU cc_start: 0.7903 (mt) cc_final: 0.7416 (mp) REVERT: F 69 LYS cc_start: 0.8225 (mppt) cc_final: 0.8024 (mmtp) REVERT: F 99 GLU cc_start: 0.7944 (tp30) cc_final: 0.7618 (tp30) REVERT: F 160 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8773 (tppt) REVERT: F 195 MET cc_start: 0.9010 (mpp) cc_final: 0.8504 (mpp) REVERT: F 218 ASP cc_start: 0.8472 (t0) cc_final: 0.8153 (t0) REVERT: F 246 ASN cc_start: 0.8946 (t0) cc_final: 0.8573 (t0) REVERT: F 289 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8417 (tpp80) REVERT: F 320 TYR cc_start: 0.8120 (p90) cc_final: 0.7655 (p90) REVERT: F 340 LYS cc_start: 0.9416 (tttp) cc_final: 0.8971 (ttpp) REVERT: F 367 VAL cc_start: 0.9056 (t) cc_final: 0.8816 (m) REVERT: F 394 VAL cc_start: 0.9423 (t) cc_final: 0.9033 (p) REVERT: F 397 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7020 (tt0) REVERT: G 168 MET cc_start: 0.7851 (mtp) cc_final: 0.7367 (mtm) REVERT: G 327 GLU cc_start: 0.7991 (tt0) cc_final: 0.7416 (tt0) REVERT: G 347 ASP cc_start: 0.7975 (t0) cc_final: 0.7617 (t0) REVERT: H 20 LEU cc_start: 0.8122 (mt) cc_final: 0.7422 (tt) REVERT: H 28 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7649 (mm110) REVERT: H 67 ASN cc_start: 0.8516 (t0) cc_final: 0.8271 (t0) REVERT: H 97 VAL cc_start: 0.9202 (m) cc_final: 0.8964 (p) REVERT: H 109 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6848 (mm-30) REVERT: H 111 GLU cc_start: 0.2829 (tp30) cc_final: 0.2464 (tp30) REVERT: I 156 MET cc_start: 0.8407 (ppp) cc_final: 0.8151 (ppp) REVERT: I 160 GLU cc_start: 0.7825 (pm20) cc_final: 0.7610 (pm20) REVERT: I 193 TYR cc_start: 0.8348 (t80) cc_final: 0.7798 (t80) REVERT: I 198 PHE cc_start: 0.8899 (m-10) cc_final: 0.8655 (m-10) REVERT: I 216 ASP cc_start: 0.8033 (t0) cc_final: 0.7740 (t0) REVERT: I 222 VAL cc_start: 0.9044 (t) cc_final: 0.8753 (m) REVERT: I 243 ASN cc_start: 0.8174 (t0) cc_final: 0.7648 (m-40) REVERT: J 37 GLU cc_start: 0.8875 (pt0) cc_final: 0.8294 (mt-10) REVERT: J 251 LEU cc_start: 0.9296 (tp) cc_final: 0.9024 (tp) REVERT: J 257 PHE cc_start: 0.9040 (m-80) cc_final: 0.8828 (m-10) REVERT: J 262 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8078 (mp0) REVERT: J 366 ILE cc_start: 0.9386 (mt) cc_final: 0.9034 (tp) REVERT: J 390 GLU cc_start: 0.8538 (tt0) cc_final: 0.8031 (tm-30) REVERT: J 396 GLN cc_start: 0.8228 (pm20) cc_final: 0.8014 (pm20) REVERT: J 399 GLN cc_start: 0.8334 (mm110) cc_final: 0.7359 (pp30) REVERT: J 404 LYS cc_start: 0.8943 (mppt) cc_final: 0.8595 (tppt) REVERT: K 30 LYS cc_start: 0.9249 (tttm) cc_final: 0.9049 (tttp) REVERT: K 54 ASN cc_start: 0.7930 (p0) cc_final: 0.7712 (p0) REVERT: K 97 LYS cc_start: 0.8528 (tptp) cc_final: 0.8307 (tptt) REVERT: K 104 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8617 (tp40) REVERT: K 141 LEU cc_start: 0.9421 (tp) cc_final: 0.8998 (tt) REVERT: K 156 ASP cc_start: 0.8424 (t0) cc_final: 0.7942 (t0) REVERT: K 158 LEU cc_start: 0.9192 (mt) cc_final: 0.8347 (mt) REVERT: K 225 GLN cc_start: 0.8436 (mt0) cc_final: 0.7960 (mt0) REVERT: K 235 LYS cc_start: 0.5291 (tttm) cc_final: 0.4754 (mmmt) REVERT: K 305 ASP cc_start: 0.8432 (t0) cc_final: 0.8101 (t0) REVERT: K 330 TRP cc_start: 0.9257 (t-100) cc_final: 0.8806 (t-100) REVERT: L 20 LEU cc_start: 0.7744 (mt) cc_final: 0.7484 (mp) REVERT: L 26 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8323 (tm-30) REVERT: L 28 GLN cc_start: 0.7402 (mm110) cc_final: 0.6974 (mm110) REVERT: L 77 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8881 (mm-30) REVERT: L 80 ASP cc_start: 0.8161 (t0) cc_final: 0.7726 (t0) REVERT: L 92 VAL cc_start: 0.8643 (t) cc_final: 0.7962 (t) REVERT: L 99 LEU cc_start: 0.9344 (mp) cc_final: 0.9055 (mt) REVERT: L 101 ASN cc_start: 0.8769 (t0) cc_final: 0.7832 (m110) REVERT: L 104 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6888 (tm-30) REVERT: L 106 PHE cc_start: 0.7778 (m-80) cc_final: 0.7255 (m-10) REVERT: L 109 GLU cc_start: 0.8571 (tt0) cc_final: 0.8196 (pm20) REVERT: L 111 GLU cc_start: 0.8771 (tt0) cc_final: 0.8542 (tp30) REVERT: M 125 CYS cc_start: 0.7748 (t) cc_final: 0.7499 (t) REVERT: M 176 THR cc_start: 0.7038 (t) cc_final: 0.6768 (t) REVERT: M 178 ASP cc_start: 0.8262 (p0) cc_final: 0.8029 (p0) REVERT: M 202 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8237 (ttt90) REVERT: M 212 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.7939 (mmm-85) REVERT: M 220 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8337 (mtm180) REVERT: M 244 GLN cc_start: 0.9146 (pm20) cc_final: 0.8899 (pm20) REVERT: N 125 HIS cc_start: 0.7111 (m-70) cc_final: 0.6894 (m90) REVERT: N 143 ARG cc_start: 0.8432 (ttm110) cc_final: 0.7915 (ttm-80) REVERT: N 144 LEU cc_start: 0.8595 (mt) cc_final: 0.8208 (mt) REVERT: N 187 TYR cc_start: 0.8903 (t80) cc_final: 0.8515 (t80) REVERT: N 321 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8617 (mtpt) REVERT: N 396 GLN cc_start: 0.9110 (tt0) cc_final: 0.8884 (tt0) REVERT: O 34 VAL cc_start: 0.9650 (t) cc_final: 0.9388 (m) REVERT: O 67 MET cc_start: 0.8162 (tpp) cc_final: 0.7838 (tpp) REVERT: O 112 THR cc_start: 0.9266 (m) cc_final: 0.9010 (p) REVERT: O 165 TYR cc_start: 0.8508 (p90) cc_final: 0.8153 (p90) REVERT: O 230 LYS cc_start: 0.8875 (pttm) cc_final: 0.8638 (pttt) REVERT: O 233 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7526 (tp-100) REVERT: O 239 ASN cc_start: 0.9131 (t0) cc_final: 0.8829 (t0) REVERT: O 242 ASP cc_start: 0.8424 (t0) cc_final: 0.8188 (t0) REVERT: P 48 LEU cc_start: 0.9446 (mt) cc_final: 0.9206 (mt) REVERT: P 53 PHE cc_start: 0.8812 (t80) cc_final: 0.8576 (t80) REVERT: P 69 GLU cc_start: 0.9003 (mp0) cc_final: 0.8780 (mp0) REVERT: P 80 ASP cc_start: 0.8267 (m-30) cc_final: 0.8021 (m-30) REVERT: P 96 GLU cc_start: 0.7537 (mp0) cc_final: 0.7241 (mp0) REVERT: Q 29 GLU cc_start: 0.8824 (tp30) cc_final: 0.8523 (mt-10) REVERT: Q 55 THR cc_start: 0.8465 (p) cc_final: 0.8160 (t) REVERT: Q 77 GLU cc_start: 0.8356 (tp30) cc_final: 0.7858 (pt0) REVERT: Q 99 LEU cc_start: 0.9040 (mt) cc_final: 0.8765 (mt) REVERT: Q 104 GLU cc_start: 0.6490 (mp0) cc_final: 0.6183 (mp0) REVERT: R 115 MET cc_start: 0.8630 (mmm) cc_final: 0.8291 (mmm) REVERT: R 116 LEU cc_start: 0.9140 (tp) cc_final: 0.8918 (tp) REVERT: R 125 CYS cc_start: 0.8888 (t) cc_final: 0.8497 (t) REVERT: R 131 LEU cc_start: 0.9344 (tp) cc_final: 0.9063 (tp) REVERT: R 133 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8407 (tttm) REVERT: R 143 ASN cc_start: 0.6204 (m110) cc_final: 0.5820 (t0) REVERT: R 160 GLU cc_start: 0.8260 (mp0) cc_final: 0.7642 (mp0) REVERT: R 161 TYR cc_start: 0.8981 (p90) cc_final: 0.8699 (p90) REVERT: R 193 TYR cc_start: 0.8587 (t80) cc_final: 0.8145 (t80) REVERT: R 207 LYS cc_start: 0.9304 (tttm) cc_final: 0.9069 (tptp) REVERT: R 209 ASP cc_start: 0.8370 (m-30) cc_final: 0.7335 (t0) REVERT: R 212 ARG cc_start: 0.8720 (mmt180) cc_final: 0.8215 (mtt-85) REVERT: R 218 ARG cc_start: 0.7601 (ptt90) cc_final: 0.6863 (ptt90) outliers start: 2 outliers final: 0 residues processed: 945 average time/residue: 0.2070 time to fit residues: 317.1089 Evaluate side-chains 769 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 769 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 369 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.0060 chunk 360 optimal weight: 6.9990 chunk 280 optimal weight: 0.5980 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 187 HIS E 243 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN J 59 GLN J 333 HIS K 96 HIS K 169 HIS K 249 HIS L 107 GLN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS N 345 HIS N 362 GLN R 143 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106543 restraints weight = 76976.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110385 restraints weight = 38682.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111783 restraints weight = 21844.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112437 restraints weight = 17299.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112264 restraints weight = 16927.210| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34852 Z= 0.125 Angle : 0.594 9.765 47484 Z= 0.307 Chirality : 0.045 0.211 5340 Planarity : 0.004 0.063 6104 Dihedral : 4.806 25.129 4744 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.13), residues: 4368 helix: 1.79 (0.24), residues: 506 sheet: -0.09 (0.14), residues: 1379 loop : -0.52 (0.13), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 303 TYR 0.019 0.001 TYR M 175 PHE 0.023 0.001 PHE B 100 TRP 0.029 0.001 TRP M 186 HIS 0.009 0.001 HIS K 358 Details of bonding type rmsd covalent geometry : bond 0.00287 (34800) covalent geometry : angle 0.59038 (47380) SS BOND : bond 0.00301 ( 52) SS BOND : angle 1.52904 ( 104) hydrogen bonds : bond 0.03347 ( 1213) hydrogen bonds : angle 5.26015 ( 3426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 925 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8745 (p0) cc_final: 0.8346 (p0) REVERT: A 240 TYR cc_start: 0.9139 (t80) cc_final: 0.8930 (t80) REVERT: A 321 LYS cc_start: 0.9560 (mtpt) cc_final: 0.9354 (mtpp) REVERT: A 433 MET cc_start: 0.7663 (mmp) cc_final: 0.7357 (tpp) REVERT: B 80 MET cc_start: 0.7626 (mmt) cc_final: 0.6560 (mmm) REVERT: B 156 ASP cc_start: 0.7703 (t0) cc_final: 0.7379 (t0) REVERT: B 239 ASN cc_start: 0.8925 (t0) cc_final: 0.8674 (t0) REVERT: E 125 CYS cc_start: 0.6938 (m) cc_final: 0.6546 (m) REVERT: E 140 LYS cc_start: 0.8673 (tmtt) cc_final: 0.8335 (tmtt) REVERT: E 186 TRP cc_start: 0.8410 (t60) cc_final: 0.7791 (t60) REVERT: E 194 GLU cc_start: 0.8689 (pp20) cc_final: 0.8017 (pp20) REVERT: E 197 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8187 (mtm110) REVERT: F 66 LEU cc_start: 0.7754 (mt) cc_final: 0.7280 (mp) REVERT: F 69 LYS cc_start: 0.8195 (mppt) cc_final: 0.7979 (mmtp) REVERT: F 99 GLU cc_start: 0.7996 (tp30) cc_final: 0.7711 (tp30) REVERT: F 160 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8740 (tppt) REVERT: F 195 MET cc_start: 0.8923 (mpp) cc_final: 0.8394 (mpp) REVERT: F 218 ASP cc_start: 0.8474 (t0) cc_final: 0.8124 (t0) REVERT: F 320 TYR cc_start: 0.8073 (p90) cc_final: 0.7647 (p90) REVERT: F 340 LYS cc_start: 0.9380 (tttp) cc_final: 0.8935 (ttpp) REVERT: F 367 VAL cc_start: 0.9028 (t) cc_final: 0.8810 (m) REVERT: F 394 VAL cc_start: 0.9390 (t) cc_final: 0.9037 (p) REVERT: F 397 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7059 (tt0) REVERT: F 402 VAL cc_start: 0.8545 (t) cc_final: 0.8270 (t) REVERT: G 80 MET cc_start: 0.8207 (tpp) cc_final: 0.7967 (tpp) REVERT: G 168 MET cc_start: 0.7844 (mtp) cc_final: 0.7358 (mtm) REVERT: G 272 HIS cc_start: 0.8366 (t-170) cc_final: 0.8101 (t-170) REVERT: G 327 GLU cc_start: 0.7931 (tt0) cc_final: 0.7360 (tt0) REVERT: G 347 ASP cc_start: 0.7956 (t0) cc_final: 0.7619 (t0) REVERT: G 351 TRP cc_start: 0.9091 (m100) cc_final: 0.8830 (m100) REVERT: G 360 TYR cc_start: 0.8665 (t80) cc_final: 0.8006 (t80) REVERT: G 393 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7474 (tpp80) REVERT: H 20 LEU cc_start: 0.8280 (mt) cc_final: 0.7551 (tt) REVERT: H 28 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7518 (mm110) REVERT: H 63 TYR cc_start: 0.7714 (m-80) cc_final: 0.7333 (m-80) REVERT: H 67 ASN cc_start: 0.8450 (t0) cc_final: 0.8192 (t0) REVERT: H 97 VAL cc_start: 0.9215 (m) cc_final: 0.9011 (p) REVERT: H 104 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7173 (tm-30) REVERT: H 109 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6791 (mm-30) REVERT: H 111 GLU cc_start: 0.2906 (tp30) cc_final: 0.2461 (tp30) REVERT: I 160 GLU cc_start: 0.7756 (pm20) cc_final: 0.7516 (pm20) REVERT: I 174 GLN cc_start: 0.8913 (mm110) cc_final: 0.8697 (mm110) REVERT: I 193 TYR cc_start: 0.8358 (t80) cc_final: 0.7804 (t80) REVERT: I 198 PHE cc_start: 0.8872 (m-10) cc_final: 0.8399 (m-10) REVERT: I 214 ILE cc_start: 0.9166 (mp) cc_final: 0.8930 (pt) REVERT: I 222 VAL cc_start: 0.9063 (t) cc_final: 0.8832 (t) REVERT: I 243 ASN cc_start: 0.8078 (t0) cc_final: 0.7539 (m-40) REVERT: J 10 VAL cc_start: 0.9384 (t) cc_final: 0.9180 (t) REVERT: J 37 GLU cc_start: 0.8897 (pt0) cc_final: 0.8321 (mt-10) REVERT: J 251 LEU cc_start: 0.9293 (tp) cc_final: 0.8992 (tp) REVERT: J 257 PHE cc_start: 0.8946 (m-80) cc_final: 0.8743 (m-10) REVERT: J 366 ILE cc_start: 0.9395 (mt) cc_final: 0.9032 (tp) REVERT: J 404 LYS cc_start: 0.8995 (mppt) cc_final: 0.8620 (tppt) REVERT: K 54 ASN cc_start: 0.7878 (p0) cc_final: 0.7664 (p0) REVERT: K 141 LEU cc_start: 0.9442 (tp) cc_final: 0.8988 (tt) REVERT: K 156 ASP cc_start: 0.8421 (t0) cc_final: 0.7854 (t0) REVERT: K 158 LEU cc_start: 0.8894 (mt) cc_final: 0.8329 (mt) REVERT: K 160 GLU cc_start: 0.8505 (pm20) cc_final: 0.8277 (tp30) REVERT: K 225 GLN cc_start: 0.8401 (mt0) cc_final: 0.7994 (mt0) REVERT: K 235 LYS cc_start: 0.5227 (tttm) cc_final: 0.4755 (mmmt) REVERT: K 240 SER cc_start: 0.9071 (t) cc_final: 0.8611 (t) REVERT: K 305 ASP cc_start: 0.8409 (t0) cc_final: 0.8070 (t0) REVERT: K 330 TRP cc_start: 0.9244 (t-100) cc_final: 0.8781 (t-100) REVERT: L 28 GLN cc_start: 0.7402 (mm110) cc_final: 0.7014 (mm110) REVERT: L 79 ILE cc_start: 0.8458 (mm) cc_final: 0.8225 (mm) REVERT: L 92 VAL cc_start: 0.8595 (t) cc_final: 0.7865 (t) REVERT: L 99 LEU cc_start: 0.9306 (mp) cc_final: 0.9030 (mt) REVERT: L 101 ASN cc_start: 0.8825 (t0) cc_final: 0.7916 (m110) REVERT: L 104 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6725 (tm-30) REVERT: L 106 PHE cc_start: 0.7740 (m-80) cc_final: 0.7220 (m-10) REVERT: L 109 GLU cc_start: 0.8488 (tt0) cc_final: 0.8177 (pm20) REVERT: L 111 GLU cc_start: 0.8712 (tt0) cc_final: 0.8495 (tp30) REVERT: M 125 CYS cc_start: 0.7918 (t) cc_final: 0.7625 (t) REVERT: M 176 THR cc_start: 0.7273 (t) cc_final: 0.5541 (m) REVERT: M 178 ASP cc_start: 0.8173 (p0) cc_final: 0.7813 (p0) REVERT: M 202 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8299 (ttt90) REVERT: M 212 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7807 (mmm-85) REVERT: M 220 ARG cc_start: 0.8515 (mtm180) cc_final: 0.7546 (mtm180) REVERT: N 144 LEU cc_start: 0.8544 (mt) cc_final: 0.8205 (mt) REVERT: N 187 TYR cc_start: 0.8840 (t80) cc_final: 0.8429 (t80) REVERT: N 298 GLU cc_start: 0.8868 (pm20) cc_final: 0.8436 (pm20) REVERT: N 321 LYS cc_start: 0.9173 (mtpp) cc_final: 0.8586 (mtmm) REVERT: N 396 GLN cc_start: 0.9128 (tt0) cc_final: 0.8879 (tt0) REVERT: O 34 VAL cc_start: 0.9643 (t) cc_final: 0.9368 (m) REVERT: O 67 MET cc_start: 0.8173 (tpp) cc_final: 0.7856 (tpp) REVERT: O 80 MET cc_start: 0.9189 (mmp) cc_final: 0.8894 (mmp) REVERT: O 112 THR cc_start: 0.9207 (m) cc_final: 0.9003 (p) REVERT: O 165 TYR cc_start: 0.8499 (p90) cc_final: 0.8109 (p90) REVERT: O 230 LYS cc_start: 0.8948 (pttm) cc_final: 0.8716 (pttt) REVERT: O 233 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7463 (tp-100) REVERT: O 239 ASN cc_start: 0.9098 (t0) cc_final: 0.8811 (t0) REVERT: O 242 ASP cc_start: 0.8302 (t0) cc_final: 0.8018 (t0) REVERT: P 48 LEU cc_start: 0.9465 (mt) cc_final: 0.9215 (mt) REVERT: P 53 PHE cc_start: 0.8701 (t80) cc_final: 0.8497 (t80) REVERT: P 80 ASP cc_start: 0.8295 (m-30) cc_final: 0.8079 (m-30) REVERT: Q 29 GLU cc_start: 0.8893 (tp30) cc_final: 0.8280 (mp0) REVERT: Q 55 THR cc_start: 0.8414 (p) cc_final: 0.8101 (t) REVERT: Q 77 GLU cc_start: 0.8336 (tp30) cc_final: 0.7816 (pt0) REVERT: R 115 MET cc_start: 0.8622 (mmm) cc_final: 0.8297 (mmm) REVERT: R 116 LEU cc_start: 0.9137 (tp) cc_final: 0.8931 (tp) REVERT: R 125 CYS cc_start: 0.8826 (t) cc_final: 0.8330 (t) REVERT: R 126 VAL cc_start: 0.9373 (m) cc_final: 0.9172 (m) REVERT: R 127 VAL cc_start: 0.9415 (m) cc_final: 0.9094 (m) REVERT: R 143 ASN cc_start: 0.6146 (m-40) cc_final: 0.5714 (t0) REVERT: R 160 GLU cc_start: 0.8416 (mp0) cc_final: 0.7870 (mp0) REVERT: R 197 ARG cc_start: 0.9036 (ttm-80) cc_final: 0.8525 (tpp-160) REVERT: R 207 LYS cc_start: 0.9297 (tttm) cc_final: 0.9046 (tptp) REVERT: R 209 ASP cc_start: 0.8384 (m-30) cc_final: 0.7650 (t0) REVERT: R 212 ARG cc_start: 0.8623 (mmt180) cc_final: 0.8356 (tpp-160) REVERT: R 250 LYS cc_start: 0.7729 (ttmm) cc_final: 0.7100 (mttt) outliers start: 0 outliers final: 0 residues processed: 925 average time/residue: 0.1974 time to fit residues: 297.8952 Evaluate side-chains 776 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 17 optimal weight: 0.8980 chunk 326 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 292 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 402 optimal weight: 40.0000 chunk 151 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 364 ASN B 50 GLN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN I 188 HIS J 59 GLN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105435 restraints weight = 76141.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109369 restraints weight = 38720.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110799 restraints weight = 21605.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111229 restraints weight = 17111.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111170 restraints weight = 16997.621| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34852 Z= 0.159 Angle : 0.607 9.771 47484 Z= 0.315 Chirality : 0.045 0.194 5340 Planarity : 0.005 0.068 6104 Dihedral : 4.818 23.680 4744 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.05 % Allowed : 2.09 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.13), residues: 4368 helix: 1.75 (0.24), residues: 495 sheet: -0.16 (0.13), residues: 1441 loop : -0.48 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 303 TYR 0.019 0.001 TYR J 107 PHE 0.024 0.001 PHE G 259 TRP 0.030 0.002 TRP M 186 HIS 0.010 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00364 (34800) covalent geometry : angle 0.60313 (47380) SS BOND : bond 0.00336 ( 52) SS BOND : angle 1.49550 ( 104) hydrogen bonds : bond 0.03412 ( 1213) hydrogen bonds : angle 5.20675 ( 3426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 907 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8862 (tt0) cc_final: 0.8601 (tp30) REVERT: A 100 ASN cc_start: 0.8820 (t160) cc_final: 0.8609 (t0) REVERT: A 212 ASP cc_start: 0.8702 (p0) cc_final: 0.8293 (p0) REVERT: A 238 SER cc_start: 0.9189 (t) cc_final: 0.7311 (p) REVERT: A 240 TYR cc_start: 0.9172 (t80) cc_final: 0.8804 (t80) REVERT: A 241 GLU cc_start: 0.8811 (mt-10) cc_final: 0.7940 (mt-10) REVERT: A 321 LYS cc_start: 0.9570 (mtpt) cc_final: 0.9364 (mtpp) REVERT: A 433 MET cc_start: 0.7683 (mmp) cc_final: 0.7374 (tpp) REVERT: B 80 MET cc_start: 0.7656 (mmt) cc_final: 0.6466 (mmm) REVERT: B 122 ASN cc_start: 0.6752 (OUTLIER) cc_final: 0.6118 (t0) REVERT: B 156 ASP cc_start: 0.7815 (t0) cc_final: 0.7459 (t0) REVERT: B 239 ASN cc_start: 0.8962 (t0) cc_final: 0.8656 (t0) REVERT: E 125 CYS cc_start: 0.6981 (m) cc_final: 0.6580 (m) REVERT: E 140 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8291 (tptt) REVERT: E 141 ILE cc_start: 0.8612 (tp) cc_final: 0.8221 (tp) REVERT: E 175 TYR cc_start: 0.7519 (p90) cc_final: 0.6886 (p90) REVERT: E 186 TRP cc_start: 0.8406 (t60) cc_final: 0.7761 (t60) REVERT: E 194 GLU cc_start: 0.8742 (pp20) cc_final: 0.8069 (pp20) REVERT: E 197 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8262 (mtm110) REVERT: E 220 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7837 (mtm-85) REVERT: E 250 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8126 (mtpt) REVERT: F 66 LEU cc_start: 0.7727 (mt) cc_final: 0.7303 (mp) REVERT: F 69 LYS cc_start: 0.8093 (mppt) cc_final: 0.7890 (mmtp) REVERT: F 99 GLU cc_start: 0.7984 (tp30) cc_final: 0.7735 (tp30) REVERT: F 160 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8691 (tppt) REVERT: F 195 MET cc_start: 0.8959 (mpp) cc_final: 0.8393 (mpp) REVERT: F 218 ASP cc_start: 0.8476 (t0) cc_final: 0.8150 (t0) REVERT: F 320 TYR cc_start: 0.8095 (p90) cc_final: 0.7656 (p90) REVERT: F 340 LYS cc_start: 0.9372 (tttp) cc_final: 0.8932 (ttpp) REVERT: F 362 GLN cc_start: 0.7856 (mp10) cc_final: 0.7611 (mp10) REVERT: F 367 VAL cc_start: 0.9030 (t) cc_final: 0.8811 (m) REVERT: F 394 VAL cc_start: 0.9376 (t) cc_final: 0.8936 (p) REVERT: F 402 VAL cc_start: 0.8526 (t) cc_final: 0.8243 (t) REVERT: G 80 MET cc_start: 0.8193 (tpp) cc_final: 0.7971 (tpp) REVERT: G 145 VAL cc_start: 0.9218 (m) cc_final: 0.8994 (p) REVERT: G 158 LEU cc_start: 0.7443 (mp) cc_final: 0.7086 (tp) REVERT: G 168 MET cc_start: 0.7715 (mtp) cc_final: 0.7475 (mtm) REVERT: G 217 MET cc_start: 0.8477 (mmm) cc_final: 0.7885 (mmm) REVERT: G 327 GLU cc_start: 0.7897 (tt0) cc_final: 0.7272 (tt0) REVERT: G 347 ASP cc_start: 0.8101 (t0) cc_final: 0.7759 (t0) REVERT: G 351 TRP cc_start: 0.9067 (m100) cc_final: 0.8840 (m100) REVERT: G 360 TYR cc_start: 0.8706 (t80) cc_final: 0.7988 (t80) REVERT: G 393 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7503 (tpp80) REVERT: H 20 LEU cc_start: 0.8264 (mt) cc_final: 0.7569 (tt) REVERT: H 28 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7450 (mm110) REVERT: H 63 TYR cc_start: 0.7754 (m-80) cc_final: 0.7468 (m-80) REVERT: H 67 ASN cc_start: 0.8419 (t0) cc_final: 0.8178 (t0) REVERT: H 73 LEU cc_start: 0.7139 (tp) cc_final: 0.6646 (mt) REVERT: H 97 VAL cc_start: 0.9236 (m) cc_final: 0.9002 (p) REVERT: H 100 GLU cc_start: 0.8528 (pp20) cc_final: 0.8262 (pp20) REVERT: H 104 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6852 (tm-30) REVERT: H 109 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6891 (mm-30) REVERT: H 111 GLU cc_start: 0.2781 (tp30) cc_final: 0.2313 (tp30) REVERT: I 125 CYS cc_start: 0.8850 (t) cc_final: 0.8648 (t) REVERT: I 160 GLU cc_start: 0.7775 (pm20) cc_final: 0.7071 (pm20) REVERT: I 164 VAL cc_start: 0.8753 (t) cc_final: 0.8529 (m) REVERT: I 174 GLN cc_start: 0.8849 (mm110) cc_final: 0.8642 (mm110) REVERT: I 214 ILE cc_start: 0.9115 (mp) cc_final: 0.8891 (pt) REVERT: I 222 VAL cc_start: 0.9136 (t) cc_final: 0.8908 (t) REVERT: I 243 ASN cc_start: 0.8129 (t0) cc_final: 0.7572 (m-40) REVERT: J 37 GLU cc_start: 0.8904 (pt0) cc_final: 0.8537 (pm20) REVERT: J 251 LEU cc_start: 0.9315 (tp) cc_final: 0.9061 (tp) REVERT: J 257 PHE cc_start: 0.8983 (m-80) cc_final: 0.8781 (m-10) REVERT: J 366 ILE cc_start: 0.9410 (mt) cc_final: 0.9056 (tp) REVERT: J 404 LYS cc_start: 0.8989 (mppt) cc_final: 0.8647 (tppt) REVERT: K 46 GLN cc_start: 0.8113 (tt0) cc_final: 0.7432 (tt0) REVERT: K 54 ASN cc_start: 0.7913 (p0) cc_final: 0.7684 (p0) REVERT: K 55 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8141 (tm-30) REVERT: K 141 LEU cc_start: 0.9417 (tp) cc_final: 0.8946 (tt) REVERT: K 156 ASP cc_start: 0.8455 (t0) cc_final: 0.7839 (t0) REVERT: K 158 LEU cc_start: 0.9034 (mt) cc_final: 0.8390 (mt) REVERT: K 235 LYS cc_start: 0.5498 (tttm) cc_final: 0.5009 (mmmt) REVERT: K 240 SER cc_start: 0.9023 (t) cc_final: 0.8214 (t) REVERT: K 305 ASP cc_start: 0.8459 (t0) cc_final: 0.8108 (t0) REVERT: K 330 TRP cc_start: 0.9245 (t-100) cc_final: 0.8834 (t-100) REVERT: L 20 LEU cc_start: 0.6929 (mp) cc_final: 0.6433 (mp) REVERT: L 28 GLN cc_start: 0.7570 (mm110) cc_final: 0.7130 (mm110) REVERT: L 72 VAL cc_start: 0.8542 (t) cc_final: 0.8333 (t) REVERT: L 80 ASP cc_start: 0.8743 (t70) cc_final: 0.8311 (t0) REVERT: L 92 VAL cc_start: 0.8551 (t) cc_final: 0.7856 (t) REVERT: L 101 ASN cc_start: 0.8872 (t0) cc_final: 0.7994 (m110) REVERT: L 104 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6676 (tm-30) REVERT: L 106 PHE cc_start: 0.7694 (m-80) cc_final: 0.7154 (m-10) REVERT: L 109 GLU cc_start: 0.8527 (tt0) cc_final: 0.8249 (pm20) REVERT: M 125 CYS cc_start: 0.7826 (t) cc_final: 0.7544 (t) REVERT: M 176 THR cc_start: 0.7267 (t) cc_final: 0.5361 (m) REVERT: M 178 ASP cc_start: 0.8273 (p0) cc_final: 0.8047 (p0) REVERT: M 202 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8276 (ttt90) REVERT: M 220 ARG cc_start: 0.8577 (mtm180) cc_final: 0.7684 (mtm180) REVERT: N 66 LEU cc_start: 0.9129 (mt) cc_final: 0.8411 (mt) REVERT: N 143 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7772 (mmm-85) REVERT: N 144 LEU cc_start: 0.8585 (mt) cc_final: 0.8119 (mt) REVERT: N 187 TYR cc_start: 0.8832 (t80) cc_final: 0.8402 (t80) REVERT: N 321 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8689 (mtpt) REVERT: N 396 GLN cc_start: 0.9149 (tt0) cc_final: 0.8902 (tt0) REVERT: O 34 VAL cc_start: 0.9650 (t) cc_final: 0.9369 (m) REVERT: O 67 MET cc_start: 0.8208 (tpp) cc_final: 0.7882 (tpp) REVERT: O 80 MET cc_start: 0.9142 (mmp) cc_final: 0.8897 (mmp) REVERT: O 112 THR cc_start: 0.9228 (m) cc_final: 0.8996 (p) REVERT: O 165 TYR cc_start: 0.8519 (p90) cc_final: 0.8109 (p90) REVERT: O 230 LYS cc_start: 0.8982 (pttm) cc_final: 0.8735 (pttt) REVERT: O 233 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7464 (tp-100) REVERT: O 239 ASN cc_start: 0.9112 (t0) cc_final: 0.8846 (t0) REVERT: P 48 LEU cc_start: 0.9447 (mt) cc_final: 0.9191 (mt) REVERT: P 53 PHE cc_start: 0.8705 (t80) cc_final: 0.8479 (t80) REVERT: P 80 ASP cc_start: 0.8570 (m-30) cc_final: 0.8186 (m-30) REVERT: P 82 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8039 (pm20) REVERT: Q 55 THR cc_start: 0.8395 (p) cc_final: 0.8079 (t) REVERT: Q 77 GLU cc_start: 0.8253 (tp30) cc_final: 0.7722 (pt0) REVERT: R 116 LEU cc_start: 0.9122 (tp) cc_final: 0.8695 (tp) REVERT: R 125 CYS cc_start: 0.8905 (t) cc_final: 0.8520 (t) REVERT: R 126 VAL cc_start: 0.9352 (m) cc_final: 0.9116 (m) REVERT: R 132 MET cc_start: 0.8503 (mmt) cc_final: 0.8287 (mmp) REVERT: R 160 GLU cc_start: 0.8399 (mp0) cc_final: 0.7697 (mp0) REVERT: R 193 TYR cc_start: 0.8483 (t80) cc_final: 0.8134 (t80) REVERT: R 197 ARG cc_start: 0.8975 (ttm-80) cc_final: 0.8611 (tpp-160) REVERT: R 207 LYS cc_start: 0.9318 (tttm) cc_final: 0.9062 (tptp) REVERT: R 209 ASP cc_start: 0.8426 (m-30) cc_final: 0.7619 (t0) REVERT: R 212 ARG cc_start: 0.8598 (mmt180) cc_final: 0.8360 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 908 average time/residue: 0.2052 time to fit residues: 305.1876 Evaluate side-chains 743 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 742 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 316 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 104 optimal weight: 0.0870 chunk 146 optimal weight: 9.9990 chunk 322 optimal weight: 0.0270 chunk 354 optimal weight: 10.0000 chunk 416 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 401 optimal weight: 30.0000 chunk 418 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN J 59 GLN ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS R 143 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.141791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104096 restraints weight = 76594.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107999 restraints weight = 38076.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109384 restraints weight = 21077.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109796 restraints weight = 16865.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109809 restraints weight = 16505.383| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34852 Z= 0.191 Angle : 0.642 10.605 47484 Z= 0.334 Chirality : 0.046 0.205 5340 Planarity : 0.005 0.058 6104 Dihedral : 4.926 28.241 4744 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.03 % Allowed : 1.79 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.13), residues: 4368 helix: 1.72 (0.24), residues: 495 sheet: -0.11 (0.14), residues: 1429 loop : -0.58 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 303 TYR 0.023 0.002 TYR R 175 PHE 0.037 0.002 PHE K 280 TRP 0.035 0.002 TRP M 186 HIS 0.022 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00433 (34800) covalent geometry : angle 0.63551 (47380) SS BOND : bond 0.00357 ( 52) SS BOND : angle 2.03283 ( 104) hydrogen bonds : bond 0.03529 ( 1213) hydrogen bonds : angle 5.20915 ( 3426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 871 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8640 (mtm) cc_final: 0.8301 (mtp) REVERT: A 212 ASP cc_start: 0.8755 (p0) cc_final: 0.8318 (p0) REVERT: A 238 SER cc_start: 0.9206 (t) cc_final: 0.8581 (p) REVERT: A 321 LYS cc_start: 0.9606 (mtpt) cc_final: 0.9397 (mtpp) REVERT: A 433 MET cc_start: 0.7759 (mmp) cc_final: 0.7504 (tpp) REVERT: B 80 MET cc_start: 0.7703 (mmt) cc_final: 0.6713 (mmm) REVERT: B 156 ASP cc_start: 0.7798 (t0) cc_final: 0.7426 (t0) REVERT: B 239 ASN cc_start: 0.9030 (t0) cc_final: 0.8773 (t0) REVERT: E 125 CYS cc_start: 0.6863 (m) cc_final: 0.6471 (m) REVERT: E 141 ILE cc_start: 0.8629 (tp) cc_final: 0.8041 (tp) REVERT: E 156 MET cc_start: 0.8978 (ppp) cc_final: 0.8622 (ppp) REVERT: E 186 TRP cc_start: 0.8346 (t60) cc_final: 0.7700 (t60) REVERT: E 197 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8292 (mtm110) REVERT: E 250 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8055 (mtpt) REVERT: F 43 ASN cc_start: 0.8919 (t0) cc_final: 0.8706 (t0) REVERT: F 99 GLU cc_start: 0.8040 (tp30) cc_final: 0.7733 (tp30) REVERT: F 143 ARG cc_start: 0.9044 (mmt-90) cc_final: 0.8840 (mmt-90) REVERT: F 160 LYS cc_start: 0.8955 (ttpp) cc_final: 0.8711 (tppt) REVERT: F 195 MET cc_start: 0.8984 (mpp) cc_final: 0.8330 (mpp) REVERT: F 218 ASP cc_start: 0.8536 (t0) cc_final: 0.8209 (t0) REVERT: F 320 TYR cc_start: 0.8061 (p90) cc_final: 0.7585 (p90) REVERT: F 340 LYS cc_start: 0.9359 (tttp) cc_final: 0.8908 (ttpp) REVERT: F 369 LEU cc_start: 0.8822 (tp) cc_final: 0.8568 (tt) REVERT: F 372 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8722 (ttpt) REVERT: F 394 VAL cc_start: 0.9282 (t) cc_final: 0.8842 (p) REVERT: G 37 GLU cc_start: 0.8821 (mm-30) cc_final: 0.7729 (tm-30) REVERT: G 80 MET cc_start: 0.8299 (tpp) cc_final: 0.8094 (tpp) REVERT: G 168 MET cc_start: 0.7886 (mtp) cc_final: 0.7459 (mtm) REVERT: G 327 GLU cc_start: 0.7965 (tt0) cc_final: 0.7416 (tt0) REVERT: G 347 ASP cc_start: 0.8084 (t0) cc_final: 0.7656 (t0) REVERT: G 351 TRP cc_start: 0.9000 (m100) cc_final: 0.8795 (m100) REVERT: G 360 TYR cc_start: 0.8707 (t80) cc_final: 0.8006 (t80) REVERT: G 393 ARG cc_start: 0.8133 (ttt90) cc_final: 0.7352 (tpp80) REVERT: H 28 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7470 (mm110) REVERT: H 67 ASN cc_start: 0.8482 (t0) cc_final: 0.8214 (t0) REVERT: H 97 VAL cc_start: 0.9242 (m) cc_final: 0.8947 (p) REVERT: H 104 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7030 (tm-30) REVERT: H 109 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6891 (mm-30) REVERT: H 111 GLU cc_start: 0.3290 (tp30) cc_final: 0.2721 (tp30) REVERT: I 125 CYS cc_start: 0.8872 (t) cc_final: 0.8671 (t) REVERT: I 144 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8453 (tm-30) REVERT: I 164 VAL cc_start: 0.8761 (t) cc_final: 0.8549 (m) REVERT: I 193 TYR cc_start: 0.8529 (t80) cc_final: 0.7830 (t80) REVERT: I 198 PHE cc_start: 0.8951 (m-10) cc_final: 0.8323 (m-10) REVERT: I 214 ILE cc_start: 0.9123 (mp) cc_final: 0.8885 (pt) REVERT: I 222 VAL cc_start: 0.9160 (t) cc_final: 0.8955 (t) REVERT: I 243 ASN cc_start: 0.8177 (t0) cc_final: 0.7611 (m-40) REVERT: J 37 GLU cc_start: 0.8946 (pt0) cc_final: 0.8569 (pm20) REVERT: J 251 LEU cc_start: 0.9336 (tp) cc_final: 0.9085 (tp) REVERT: J 257 PHE cc_start: 0.9015 (m-80) cc_final: 0.8810 (m-10) REVERT: J 366 ILE cc_start: 0.9403 (mt) cc_final: 0.9004 (tp) REVERT: J 404 LYS cc_start: 0.8970 (mppt) cc_final: 0.8616 (tppt) REVERT: K 46 GLN cc_start: 0.8157 (tt0) cc_final: 0.7527 (tt0) REVERT: K 54 ASN cc_start: 0.7950 (p0) cc_final: 0.7736 (p0) REVERT: K 104 GLN cc_start: 0.9033 (tp40) cc_final: 0.8824 (tp40) REVERT: K 141 LEU cc_start: 0.9434 (tp) cc_final: 0.8996 (tt) REVERT: K 156 ASP cc_start: 0.8493 (t0) cc_final: 0.7949 (t0) REVERT: K 158 LEU cc_start: 0.9024 (mt) cc_final: 0.8288 (mt) REVERT: K 160 GLU cc_start: 0.8552 (pm20) cc_final: 0.8328 (tp30) REVERT: K 235 LYS cc_start: 0.5565 (tttm) cc_final: 0.5356 (tptm) REVERT: K 240 SER cc_start: 0.9080 (t) cc_final: 0.8170 (t) REVERT: K 294 LEU cc_start: 0.9503 (tp) cc_final: 0.9269 (tp) REVERT: K 305 ASP cc_start: 0.8506 (t0) cc_final: 0.8165 (t0) REVERT: K 330 TRP cc_start: 0.9262 (t-100) cc_final: 0.8814 (t-100) REVERT: K 334 GLU cc_start: 0.8566 (mp0) cc_final: 0.8285 (mp0) REVERT: L 20 LEU cc_start: 0.6872 (mp) cc_final: 0.6272 (mp) REVERT: L 26 GLU cc_start: 0.8552 (tp30) cc_final: 0.8323 (tp30) REVERT: L 28 GLN cc_start: 0.7398 (mm110) cc_final: 0.7047 (mm110) REVERT: L 65 ASP cc_start: 0.7891 (m-30) cc_final: 0.7572 (t70) REVERT: L 72 VAL cc_start: 0.8536 (t) cc_final: 0.8331 (t) REVERT: L 80 ASP cc_start: 0.8761 (t70) cc_final: 0.8394 (t0) REVERT: L 101 ASN cc_start: 0.8904 (t0) cc_final: 0.8018 (m110) REVERT: L 104 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6680 (tm-30) REVERT: L 109 GLU cc_start: 0.8620 (tt0) cc_final: 0.8301 (pm20) REVERT: M 125 CYS cc_start: 0.7869 (t) cc_final: 0.7633 (t) REVERT: M 176 THR cc_start: 0.7327 (t) cc_final: 0.5365 (m) REVERT: M 178 ASP cc_start: 0.8194 (p0) cc_final: 0.7977 (p0) REVERT: M 194 GLU cc_start: 0.7390 (pp20) cc_final: 0.6910 (pp20) REVERT: M 195 ASN cc_start: 0.8849 (m-40) cc_final: 0.8631 (m110) REVERT: M 202 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8223 (ttt90) REVERT: M 220 ARG cc_start: 0.8600 (mtm180) cc_final: 0.7677 (mtm180) REVERT: N 66 LEU cc_start: 0.9194 (mt) cc_final: 0.8511 (mt) REVERT: N 117 ASP cc_start: 0.9000 (t0) cc_final: 0.8720 (t0) REVERT: N 143 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7798 (mmm-85) REVERT: N 144 LEU cc_start: 0.8655 (mt) cc_final: 0.8236 (mt) REVERT: N 174 ASP cc_start: 0.7855 (p0) cc_final: 0.7285 (p0) REVERT: N 186 ASN cc_start: 0.9139 (m-40) cc_final: 0.8575 (m-40) REVERT: N 187 TYR cc_start: 0.8776 (t80) cc_final: 0.8188 (t80) REVERT: N 188 ASP cc_start: 0.9010 (t70) cc_final: 0.8673 (t0) REVERT: N 230 HIS cc_start: 0.8840 (p90) cc_final: 0.8609 (p90) REVERT: N 321 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8780 (mtmm) REVERT: N 396 GLN cc_start: 0.9246 (tt0) cc_final: 0.9031 (tt0) REVERT: O 34 VAL cc_start: 0.9652 (t) cc_final: 0.9348 (m) REVERT: O 67 MET cc_start: 0.8353 (tpp) cc_final: 0.8010 (tpp) REVERT: O 80 MET cc_start: 0.9177 (mmp) cc_final: 0.8976 (mmp) REVERT: O 125 THR cc_start: 0.9326 (m) cc_final: 0.8771 (p) REVERT: O 165 TYR cc_start: 0.8571 (p90) cc_final: 0.8091 (p90) REVERT: O 230 LYS cc_start: 0.8947 (pttm) cc_final: 0.8737 (pttt) REVERT: O 233 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7447 (tm-30) REVERT: P 48 LEU cc_start: 0.9439 (mt) cc_final: 0.9117 (mt) REVERT: P 80 ASP cc_start: 0.8583 (m-30) cc_final: 0.8199 (m-30) REVERT: P 82 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8021 (pm20) REVERT: Q 55 THR cc_start: 0.8416 (p) cc_final: 0.8091 (t) REVERT: Q 77 GLU cc_start: 0.8279 (tp30) cc_final: 0.7700 (pt0) REVERT: Q 99 LEU cc_start: 0.8990 (mt) cc_final: 0.8705 (mt) REVERT: R 115 MET cc_start: 0.8745 (mmm) cc_final: 0.8390 (mmm) REVERT: R 125 CYS cc_start: 0.9020 (t) cc_final: 0.8510 (t) REVERT: R 126 VAL cc_start: 0.9318 (m) cc_final: 0.9103 (m) REVERT: R 132 MET cc_start: 0.8568 (mmt) cc_final: 0.8346 (mmp) REVERT: R 160 GLU cc_start: 0.8379 (mp0) cc_final: 0.7733 (mp0) REVERT: R 197 ARG cc_start: 0.9009 (ttm-80) cc_final: 0.8578 (tpp-160) REVERT: R 207 LYS cc_start: 0.9352 (tttm) cc_final: 0.9062 (tptp) REVERT: R 209 ASP cc_start: 0.8416 (m-30) cc_final: 0.7800 (t0) REVERT: R 212 ARG cc_start: 0.8541 (mmt180) cc_final: 0.8195 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 871 average time/residue: 0.1987 time to fit residues: 283.7568 Evaluate side-chains 752 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 752 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 363 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 377 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 367 optimal weight: 0.8980 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 357 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 377 ASN B 73 HIS E 188 HIS E 243 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN J 345 HIS J 399 GLN K 33 ASN ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103776 restraints weight = 76991.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107880 restraints weight = 38990.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108805 restraints weight = 21396.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109273 restraints weight = 18254.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109344 restraints weight = 17123.846| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34852 Z= 0.195 Angle : 0.651 17.374 47484 Z= 0.336 Chirality : 0.045 0.260 5340 Planarity : 0.005 0.057 6104 Dihedral : 4.930 27.896 4744 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.03 % Allowed : 1.18 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.13), residues: 4368 helix: 1.75 (0.24), residues: 495 sheet: -0.20 (0.13), residues: 1457 loop : -0.64 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 303 TYR 0.020 0.002 TYR R 175 PHE 0.029 0.002 PHE L 106 TRP 0.039 0.002 TRP M 186 HIS 0.018 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00444 (34800) covalent geometry : angle 0.64611 (47380) SS BOND : bond 0.00386 ( 52) SS BOND : angle 1.87709 ( 104) hydrogen bonds : bond 0.03577 ( 1213) hydrogen bonds : angle 5.25712 ( 3426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 882 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8758 (mtm) cc_final: 0.8401 (mtp) REVERT: A 212 ASP cc_start: 0.8765 (p0) cc_final: 0.8303 (p0) REVERT: A 218 ASP cc_start: 0.8331 (t0) cc_final: 0.8100 (t0) REVERT: A 238 SER cc_start: 0.9178 (t) cc_final: 0.8493 (p) REVERT: A 321 LYS cc_start: 0.9626 (mtpt) cc_final: 0.9419 (mtpp) REVERT: A 433 MET cc_start: 0.7780 (mmp) cc_final: 0.7517 (tpp) REVERT: B 39 ASP cc_start: 0.8795 (m-30) cc_final: 0.8576 (m-30) REVERT: B 80 MET cc_start: 0.7667 (mmt) cc_final: 0.6677 (mmm) REVERT: B 156 ASP cc_start: 0.7836 (t0) cc_final: 0.7596 (t0) REVERT: B 217 MET cc_start: 0.8594 (tpp) cc_final: 0.8332 (tpp) REVERT: B 239 ASN cc_start: 0.8985 (t0) cc_final: 0.8752 (t0) REVERT: E 125 CYS cc_start: 0.6774 (m) cc_final: 0.6433 (m) REVERT: E 140 LYS cc_start: 0.8681 (tptp) cc_final: 0.8455 (tptt) REVERT: E 141 ILE cc_start: 0.8418 (tp) cc_final: 0.8083 (tp) REVERT: E 153 LYS cc_start: 0.8309 (tmmt) cc_final: 0.7854 (tmmt) REVERT: E 185 ASN cc_start: 0.8824 (m-40) cc_final: 0.8575 (m-40) REVERT: E 186 TRP cc_start: 0.8217 (t60) cc_final: 0.7665 (t60) REVERT: E 197 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.8505 (mtm110) REVERT: E 220 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7738 (mtm-85) REVERT: E 250 LYS cc_start: 0.8470 (ttpp) cc_final: 0.7977 (mtpt) REVERT: F 43 ASN cc_start: 0.8941 (t0) cc_final: 0.8706 (t0) REVERT: F 99 GLU cc_start: 0.8050 (tp30) cc_final: 0.7710 (tp30) REVERT: F 117 ASP cc_start: 0.8933 (t0) cc_final: 0.8528 (t0) REVERT: F 143 ARG cc_start: 0.9024 (mmt-90) cc_final: 0.8783 (mmt-90) REVERT: F 195 MET cc_start: 0.9024 (mpp) cc_final: 0.8362 (mpp) REVERT: F 218 ASP cc_start: 0.8554 (t0) cc_final: 0.8206 (t0) REVERT: F 311 ASP cc_start: 0.8485 (p0) cc_final: 0.8167 (p0) REVERT: F 320 TYR cc_start: 0.8056 (p90) cc_final: 0.7568 (p90) REVERT: F 340 LYS cc_start: 0.9345 (tttp) cc_final: 0.8888 (ttpp) REVERT: F 362 GLN cc_start: 0.7957 (mp10) cc_final: 0.7729 (mp10) REVERT: F 372 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8706 (ttpt) REVERT: F 394 VAL cc_start: 0.9273 (t) cc_final: 0.8836 (p) REVERT: G 37 GLU cc_start: 0.8774 (mm-30) cc_final: 0.7708 (tm-30) REVERT: G 168 MET cc_start: 0.7899 (mtp) cc_final: 0.7401 (mtm) REVERT: G 217 MET cc_start: 0.8491 (mmm) cc_final: 0.7858 (mmm) REVERT: G 327 GLU cc_start: 0.7926 (tt0) cc_final: 0.7450 (tt0) REVERT: G 347 ASP cc_start: 0.8157 (t0) cc_final: 0.7723 (t0) REVERT: G 360 TYR cc_start: 0.8707 (t80) cc_final: 0.8018 (t80) REVERT: G 393 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7359 (tpp80) REVERT: H 28 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7409 (mm110) REVERT: H 67 ASN cc_start: 0.8500 (t0) cc_final: 0.8234 (t0) REVERT: H 73 LEU cc_start: 0.7339 (tt) cc_final: 0.6611 (mp) REVERT: H 97 VAL cc_start: 0.9190 (m) cc_final: 0.8900 (p) REVERT: H 104 GLU cc_start: 0.7903 (mt-10) cc_final: 0.6967 (tp30) REVERT: H 109 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6533 (mm-30) REVERT: H 111 GLU cc_start: 0.3337 (tp30) cc_final: 0.2820 (tp30) REVERT: I 125 CYS cc_start: 0.8783 (t) cc_final: 0.8493 (t) REVERT: I 144 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8455 (tm-30) REVERT: I 193 TYR cc_start: 0.8497 (t80) cc_final: 0.7784 (t80) REVERT: I 198 PHE cc_start: 0.9004 (m-10) cc_final: 0.8362 (m-10) REVERT: I 214 ILE cc_start: 0.9100 (mp) cc_final: 0.8844 (pt) REVERT: I 243 ASN cc_start: 0.8160 (t0) cc_final: 0.7608 (m-40) REVERT: I 247 VAL cc_start: 0.8980 (t) cc_final: 0.8518 (t) REVERT: J 37 GLU cc_start: 0.8988 (pt0) cc_final: 0.8590 (pm20) REVERT: J 251 LEU cc_start: 0.9358 (tp) cc_final: 0.9102 (tp) REVERT: J 257 PHE cc_start: 0.8953 (m-80) cc_final: 0.8746 (m-10) REVERT: J 366 ILE cc_start: 0.9399 (mt) cc_final: 0.8991 (tp) REVERT: J 390 GLU cc_start: 0.8680 (tt0) cc_final: 0.7680 (tm-30) REVERT: J 404 LYS cc_start: 0.8948 (mppt) cc_final: 0.8628 (tppt) REVERT: K 40 ASP cc_start: 0.8827 (p0) cc_final: 0.8568 (p0) REVERT: K 104 GLN cc_start: 0.9016 (tp40) cc_final: 0.8728 (tp40) REVERT: K 156 ASP cc_start: 0.8499 (t0) cc_final: 0.7975 (t0) REVERT: K 158 LEU cc_start: 0.9002 (mt) cc_final: 0.8284 (mt) REVERT: K 305 ASP cc_start: 0.8529 (t0) cc_final: 0.8195 (t0) REVERT: K 330 TRP cc_start: 0.9303 (t-100) cc_final: 0.8855 (t-100) REVERT: K 334 GLU cc_start: 0.8659 (mp0) cc_final: 0.8370 (mp0) REVERT: K 354 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8394 (mt-10) REVERT: K 400 TYR cc_start: 0.8856 (m-80) cc_final: 0.8590 (m-80) REVERT: L 26 GLU cc_start: 0.8567 (tp30) cc_final: 0.8349 (tp30) REVERT: L 28 GLN cc_start: 0.7389 (mm110) cc_final: 0.6883 (mm110) REVERT: L 80 ASP cc_start: 0.8740 (t70) cc_final: 0.8363 (t0) REVERT: L 99 LEU cc_start: 0.9111 (mt) cc_final: 0.8722 (mt) REVERT: L 101 ASN cc_start: 0.8804 (t0) cc_final: 0.7885 (m110) REVERT: M 125 CYS cc_start: 0.8073 (t) cc_final: 0.7725 (t) REVERT: M 202 ARG cc_start: 0.8736 (ttp80) cc_final: 0.8149 (ttt90) REVERT: N 66 LEU cc_start: 0.9205 (mt) cc_final: 0.8554 (mt) REVERT: N 143 ARG cc_start: 0.8394 (ttm110) cc_final: 0.7846 (mmm-85) REVERT: N 187 TYR cc_start: 0.8770 (t80) cc_final: 0.8209 (t80) REVERT: N 321 LYS cc_start: 0.9171 (mtpp) cc_final: 0.8751 (mtmm) REVERT: N 396 GLN cc_start: 0.9207 (tt0) cc_final: 0.8978 (tt0) REVERT: O 34 VAL cc_start: 0.9660 (t) cc_final: 0.9368 (m) REVERT: O 50 GLN cc_start: 0.7427 (mp10) cc_final: 0.7002 (mm-40) REVERT: O 67 MET cc_start: 0.8425 (tpp) cc_final: 0.8020 (tpp) REVERT: O 125 THR cc_start: 0.9331 (m) cc_final: 0.8787 (p) REVERT: O 165 TYR cc_start: 0.8627 (p90) cc_final: 0.8411 (p90) REVERT: O 233 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7451 (tm-30) REVERT: P 48 LEU cc_start: 0.9427 (mt) cc_final: 0.9183 (mt) REVERT: P 53 PHE cc_start: 0.8652 (t80) cc_final: 0.8440 (t80) REVERT: P 80 ASP cc_start: 0.8644 (m-30) cc_final: 0.8248 (m-30) REVERT: P 82 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8010 (pm20) REVERT: Q 77 GLU cc_start: 0.8276 (tp30) cc_final: 0.7668 (pt0) REVERT: Q 99 LEU cc_start: 0.8956 (mt) cc_final: 0.8700 (mt) REVERT: R 115 MET cc_start: 0.8671 (mmm) cc_final: 0.8388 (mmm) REVERT: R 125 CYS cc_start: 0.9056 (t) cc_final: 0.8537 (t) REVERT: R 126 VAL cc_start: 0.9314 (m) cc_final: 0.9102 (m) REVERT: R 160 GLU cc_start: 0.8379 (mp0) cc_final: 0.7703 (mp0) REVERT: R 197 ARG cc_start: 0.9044 (ttm-80) cc_final: 0.8580 (tpp-160) REVERT: R 207 LYS cc_start: 0.9368 (tttm) cc_final: 0.9066 (tptp) REVERT: R 209 ASP cc_start: 0.8358 (m-30) cc_final: 0.7941 (t0) REVERT: R 212 ARG cc_start: 0.8605 (mmt180) cc_final: 0.7978 (tpp-160) REVERT: R 243 ASN cc_start: 0.8015 (t0) cc_final: 0.7725 (t0) outliers start: 1 outliers final: 0 residues processed: 882 average time/residue: 0.2109 time to fit residues: 305.8063 Evaluate side-chains 736 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 736 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 92 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 193 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 377 ASN B 157 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.142486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104700 restraints weight = 76944.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108521 restraints weight = 40207.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109469 restraints weight = 23567.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110157 restraints weight = 19057.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110257 restraints weight = 17524.774| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34852 Z= 0.146 Angle : 0.635 12.981 47484 Z= 0.327 Chirality : 0.045 0.279 5340 Planarity : 0.005 0.058 6104 Dihedral : 4.892 26.048 4744 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.13), residues: 4368 helix: 1.74 (0.24), residues: 495 sheet: -0.19 (0.14), residues: 1445 loop : -0.60 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 303 TYR 0.019 0.001 TYR R 193 PHE 0.031 0.001 PHE L 106 TRP 0.042 0.002 TRP M 186 HIS 0.008 0.001 HIS J 52 Details of bonding type rmsd covalent geometry : bond 0.00337 (34800) covalent geometry : angle 0.63088 (47380) SS BOND : bond 0.00428 ( 52) SS BOND : angle 1.73291 ( 104) hydrogen bonds : bond 0.03436 ( 1213) hydrogen bonds : angle 5.17451 ( 3426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 866 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8790 (mtm) cc_final: 0.8398 (mtp) REVERT: A 212 ASP cc_start: 0.8725 (p0) cc_final: 0.8315 (p0) REVERT: A 238 SER cc_start: 0.9076 (t) cc_final: 0.7631 (t) REVERT: A 241 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8397 (mt-10) REVERT: A 320 TYR cc_start: 0.8695 (p90) cc_final: 0.8333 (p90) REVERT: A 433 MET cc_start: 0.7768 (mmp) cc_final: 0.7511 (tpp) REVERT: B 39 ASP cc_start: 0.8734 (m-30) cc_final: 0.8501 (m-30) REVERT: B 80 MET cc_start: 0.7708 (mmt) cc_final: 0.6710 (mmm) REVERT: B 156 ASP cc_start: 0.7692 (t0) cc_final: 0.7263 (t0) REVERT: B 159 LYS cc_start: 0.8580 (pttt) cc_final: 0.8282 (ptpp) REVERT: B 217 MET cc_start: 0.8547 (tpp) cc_final: 0.8307 (tpp) REVERT: B 239 ASN cc_start: 0.8952 (t0) cc_final: 0.8743 (t0) REVERT: B 272 HIS cc_start: 0.8848 (t70) cc_final: 0.8117 (t-170) REVERT: E 125 CYS cc_start: 0.6973 (m) cc_final: 0.6600 (m) REVERT: E 140 LYS cc_start: 0.8600 (tptp) cc_final: 0.8037 (tptt) REVERT: E 153 LYS cc_start: 0.8310 (tmmt) cc_final: 0.8106 (tmmt) REVERT: E 175 TYR cc_start: 0.7587 (p90) cc_final: 0.7189 (p90) REVERT: E 185 ASN cc_start: 0.8837 (m-40) cc_final: 0.8571 (m-40) REVERT: E 186 TRP cc_start: 0.8130 (t60) cc_final: 0.7787 (t60) REVERT: E 197 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8530 (mtm110) REVERT: E 198 PHE cc_start: 0.8416 (m-80) cc_final: 0.8207 (m-10) REVERT: E 220 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: E 250 LYS cc_start: 0.8487 (ttpp) cc_final: 0.7948 (mtpt) REVERT: F 43 ASN cc_start: 0.8914 (t0) cc_final: 0.8686 (t0) REVERT: F 99 GLU cc_start: 0.8061 (tp30) cc_final: 0.7752 (tp30) REVERT: F 143 ARG cc_start: 0.9009 (mmt-90) cc_final: 0.8786 (mmt-90) REVERT: F 195 MET cc_start: 0.9022 (mpp) cc_final: 0.8328 (mpp) REVERT: F 218 ASP cc_start: 0.8470 (t0) cc_final: 0.8162 (t0) REVERT: F 320 TYR cc_start: 0.8009 (p90) cc_final: 0.7709 (p90) REVERT: F 340 LYS cc_start: 0.9335 (tttp) cc_final: 0.8872 (ttpp) REVERT: F 372 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8736 (ttpt) REVERT: F 394 VAL cc_start: 0.9229 (t) cc_final: 0.8833 (p) REVERT: G 37 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8084 (tm-30) REVERT: G 67 MET cc_start: 0.8632 (tpt) cc_final: 0.8425 (tpp) REVERT: G 168 MET cc_start: 0.7934 (mtp) cc_final: 0.7489 (mtm) REVERT: G 217 MET cc_start: 0.8605 (mmm) cc_final: 0.8039 (mmm) REVERT: G 327 GLU cc_start: 0.7827 (tt0) cc_final: 0.7364 (tt0) REVERT: G 341 GLN cc_start: 0.7394 (mt0) cc_final: 0.7091 (mt0) REVERT: G 347 ASP cc_start: 0.8087 (t0) cc_final: 0.7680 (t0) REVERT: G 393 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7320 (tpp80) REVERT: H 28 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7375 (mm110) REVERT: H 48 LEU cc_start: 0.7743 (mt) cc_final: 0.7165 (tt) REVERT: H 67 ASN cc_start: 0.8527 (t0) cc_final: 0.8215 (t0) REVERT: H 97 VAL cc_start: 0.9129 (m) cc_final: 0.8779 (p) REVERT: H 104 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6957 (tp30) REVERT: H 109 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6341 (mm-30) REVERT: H 111 GLU cc_start: 0.3674 (tp30) cc_final: 0.3186 (tp30) REVERT: I 144 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8390 (tm-30) REVERT: I 193 TYR cc_start: 0.8480 (t80) cc_final: 0.7746 (t80) REVERT: I 198 PHE cc_start: 0.8982 (m-10) cc_final: 0.8546 (m-10) REVERT: I 214 ILE cc_start: 0.8987 (mp) cc_final: 0.8750 (mp) REVERT: I 222 VAL cc_start: 0.8888 (t) cc_final: 0.8570 (m) REVERT: I 243 ASN cc_start: 0.8266 (t0) cc_final: 0.7754 (m-40) REVERT: I 247 VAL cc_start: 0.9008 (t) cc_final: 0.8597 (t) REVERT: J 37 GLU cc_start: 0.8949 (pt0) cc_final: 0.8585 (pm20) REVERT: J 195 MET cc_start: 0.8825 (mpp) cc_final: 0.8595 (mpp) REVERT: J 251 LEU cc_start: 0.9339 (tp) cc_final: 0.9094 (tp) REVERT: J 257 PHE cc_start: 0.8879 (m-80) cc_final: 0.8649 (m-10) REVERT: J 366 ILE cc_start: 0.9402 (mt) cc_final: 0.9013 (tp) REVERT: J 387 ILE cc_start: 0.9274 (mm) cc_final: 0.9026 (mt) REVERT: J 390 GLU cc_start: 0.8675 (tt0) cc_final: 0.8204 (tm-30) REVERT: J 399 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7543 (pp30) REVERT: J 404 LYS cc_start: 0.8901 (mppt) cc_final: 0.8581 (tppt) REVERT: K 40 ASP cc_start: 0.8835 (p0) cc_final: 0.8588 (p0) REVERT: K 104 GLN cc_start: 0.8974 (tp40) cc_final: 0.8721 (tp40) REVERT: K 141 LEU cc_start: 0.9443 (tp) cc_final: 0.9004 (tt) REVERT: K 156 ASP cc_start: 0.8415 (t0) cc_final: 0.7946 (t0) REVERT: K 158 LEU cc_start: 0.8963 (mt) cc_final: 0.8262 (mt) REVERT: K 305 ASP cc_start: 0.8535 (t0) cc_final: 0.8195 (t0) REVERT: K 330 TRP cc_start: 0.9277 (t-100) cc_final: 0.8788 (t-100) REVERT: K 334 GLU cc_start: 0.8598 (mp0) cc_final: 0.8324 (mp0) REVERT: K 354 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8383 (mt-10) REVERT: K 400 TYR cc_start: 0.8838 (m-80) cc_final: 0.8590 (m-80) REVERT: L 28 GLN cc_start: 0.7323 (mm110) cc_final: 0.6811 (mm110) REVERT: L 54 GLN cc_start: 0.7828 (pm20) cc_final: 0.7601 (pm20) REVERT: L 69 GLU cc_start: 0.9001 (mp0) cc_final: 0.8739 (mp0) REVERT: L 80 ASP cc_start: 0.8768 (t70) cc_final: 0.8417 (t0) REVERT: L 99 LEU cc_start: 0.9119 (mt) cc_final: 0.8885 (mt) REVERT: L 101 ASN cc_start: 0.8789 (t0) cc_final: 0.7830 (m110) REVERT: L 104 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6807 (tm-30) REVERT: L 106 PHE cc_start: 0.7672 (m-80) cc_final: 0.7297 (m-80) REVERT: M 125 CYS cc_start: 0.8073 (t) cc_final: 0.7768 (t) REVERT: M 176 THR cc_start: 0.6224 (m) cc_final: 0.4558 (m) REVERT: M 178 ASP cc_start: 0.8536 (p0) cc_final: 0.8230 (p0) REVERT: M 197 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: M 202 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8271 (ttt90) REVERT: M 220 ARG cc_start: 0.8595 (mtm180) cc_final: 0.8104 (mtm180) REVERT: N 66 LEU cc_start: 0.9177 (mt) cc_final: 0.8559 (mt) REVERT: N 143 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8044 (mtp85) REVERT: N 144 LEU cc_start: 0.8631 (mt) cc_final: 0.8235 (mt) REVERT: N 174 ASP cc_start: 0.7980 (p0) cc_final: 0.6991 (p0) REVERT: N 186 ASN cc_start: 0.9128 (m-40) cc_final: 0.8779 (m-40) REVERT: N 321 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8769 (mtmm) REVERT: N 396 GLN cc_start: 0.9117 (tt0) cc_final: 0.8910 (tt0) REVERT: O 34 VAL cc_start: 0.9642 (t) cc_final: 0.9338 (m) REVERT: O 67 MET cc_start: 0.8540 (tpp) cc_final: 0.8087 (tpp) REVERT: O 80 MET cc_start: 0.9100 (mmp) cc_final: 0.8496 (mmt) REVERT: O 125 THR cc_start: 0.9319 (m) cc_final: 0.8758 (p) REVERT: O 165 TYR cc_start: 0.8528 (p90) cc_final: 0.8289 (p90) REVERT: P 48 LEU cc_start: 0.9436 (mt) cc_final: 0.9215 (mt) REVERT: P 53 PHE cc_start: 0.8651 (t80) cc_final: 0.8445 (t80) REVERT: P 80 ASP cc_start: 0.8655 (m-30) cc_final: 0.8246 (m-30) REVERT: P 82 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7977 (pm20) REVERT: P 109 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7463 (mt-10) REVERT: Q 55 THR cc_start: 0.8381 (p) cc_final: 0.8055 (t) REVERT: Q 77 GLU cc_start: 0.8233 (tp30) cc_final: 0.7637 (pt0) REVERT: Q 99 LEU cc_start: 0.8978 (mt) cc_final: 0.8710 (mt) REVERT: Q 104 GLU cc_start: 0.6664 (mp0) cc_final: 0.6440 (mp0) REVERT: R 115 MET cc_start: 0.8671 (mmm) cc_final: 0.8376 (mmm) REVERT: R 125 CYS cc_start: 0.9014 (t) cc_final: 0.8427 (t) REVERT: R 126 VAL cc_start: 0.9295 (m) cc_final: 0.9059 (m) REVERT: R 160 GLU cc_start: 0.8468 (mp0) cc_final: 0.7841 (mp0) REVERT: R 191 VAL cc_start: 0.8561 (m) cc_final: 0.8279 (p) REVERT: R 193 TYR cc_start: 0.8467 (t80) cc_final: 0.8148 (t80) REVERT: R 197 ARG cc_start: 0.9029 (ttm-80) cc_final: 0.8688 (tpp-160) REVERT: R 207 LYS cc_start: 0.9374 (tttm) cc_final: 0.9085 (tptp) REVERT: R 209 ASP cc_start: 0.8349 (m-30) cc_final: 0.7824 (t0) REVERT: R 212 ARG cc_start: 0.8629 (mmt180) cc_final: 0.8191 (mmt-90) REVERT: R 220 ARG cc_start: 0.8576 (ptm160) cc_final: 0.8138 (ptm160) REVERT: R 243 ASN cc_start: 0.7914 (t0) cc_final: 0.7677 (t0) outliers start: 1 outliers final: 0 residues processed: 866 average time/residue: 0.2218 time to fit residues: 314.7224 Evaluate side-chains 742 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 742 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 176 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 403 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 332 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 394 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 377 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN K 33 ASN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 GLN P 36 ASN R 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104541 restraints weight = 77694.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108895 restraints weight = 40840.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109442 restraints weight = 22858.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110182 restraints weight = 19314.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110289 restraints weight = 17922.992| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34852 Z= 0.175 Angle : 0.650 14.280 47484 Z= 0.334 Chirality : 0.046 0.236 5340 Planarity : 0.005 0.059 6104 Dihedral : 4.937 27.150 4744 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.13), residues: 4368 helix: 1.72 (0.24), residues: 494 sheet: -0.22 (0.13), residues: 1457 loop : -0.64 (0.13), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 303 TYR 0.025 0.001 TYR N 24 PHE 0.029 0.002 PHE L 106 TRP 0.049 0.002 TRP M 186 HIS 0.014 0.001 HIS G 349 Details of bonding type rmsd covalent geometry : bond 0.00401 (34800) covalent geometry : angle 0.64485 (47380) SS BOND : bond 0.00400 ( 52) SS BOND : angle 1.78942 ( 104) hydrogen bonds : bond 0.03500 ( 1213) hydrogen bonds : angle 5.19664 ( 3426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 849 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8825 (mtm) cc_final: 0.8383 (mtp) REVERT: A 212 ASP cc_start: 0.8724 (p0) cc_final: 0.8289 (p0) REVERT: A 238 SER cc_start: 0.9119 (t) cc_final: 0.7731 (t) REVERT: A 241 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 320 TYR cc_start: 0.8661 (p90) cc_final: 0.8425 (p90) REVERT: A 433 MET cc_start: 0.7765 (mmp) cc_final: 0.7502 (tpp) REVERT: B 15 PHE cc_start: 0.7505 (t80) cc_final: 0.7192 (t80) REVERT: B 39 ASP cc_start: 0.8746 (m-30) cc_final: 0.8523 (m-30) REVERT: B 80 MET cc_start: 0.7781 (mmt) cc_final: 0.6723 (mmm) REVERT: B 122 ASN cc_start: 0.7107 (t0) cc_final: 0.6699 (t0) REVERT: B 156 ASP cc_start: 0.7848 (t0) cc_final: 0.7514 (t0) REVERT: B 217 MET cc_start: 0.8501 (tpp) cc_final: 0.8288 (tpp) REVERT: B 239 ASN cc_start: 0.8954 (t0) cc_final: 0.8616 (m-40) REVERT: E 125 CYS cc_start: 0.6937 (m) cc_final: 0.6544 (m) REVERT: E 153 LYS cc_start: 0.8231 (tmmt) cc_final: 0.8000 (tmmt) REVERT: E 185 ASN cc_start: 0.8937 (m-40) cc_final: 0.8706 (m-40) REVERT: E 186 TRP cc_start: 0.8341 (t60) cc_final: 0.7830 (t60) REVERT: E 197 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8577 (mtm110) REVERT: E 220 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.8021 (mtm-85) REVERT: E 250 LYS cc_start: 0.8475 (ttpp) cc_final: 0.7924 (mtpt) REVERT: F 43 ASN cc_start: 0.8916 (t0) cc_final: 0.8682 (t0) REVERT: F 99 GLU cc_start: 0.8101 (tp30) cc_final: 0.7864 (tp30) REVERT: F 143 ARG cc_start: 0.9021 (mmt-90) cc_final: 0.8806 (mmt-90) REVERT: F 195 MET cc_start: 0.8963 (mpp) cc_final: 0.8274 (mpp) REVERT: F 218 ASP cc_start: 0.8491 (t0) cc_final: 0.8181 (t0) REVERT: F 320 TYR cc_start: 0.7999 (p90) cc_final: 0.7704 (p90) REVERT: F 340 LYS cc_start: 0.9326 (tttp) cc_final: 0.8863 (ttpp) REVERT: F 372 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8706 (ttpt) REVERT: F 394 VAL cc_start: 0.9293 (t) cc_final: 0.8888 (p) REVERT: F 402 VAL cc_start: 0.8597 (t) cc_final: 0.8381 (t) REVERT: G 37 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8109 (tm-30) REVERT: G 67 MET cc_start: 0.8696 (tpt) cc_final: 0.8433 (tpp) REVERT: G 71 HIS cc_start: 0.7951 (m-70) cc_final: 0.7697 (m170) REVERT: G 168 MET cc_start: 0.7768 (mtp) cc_final: 0.7424 (mtm) REVERT: G 217 MET cc_start: 0.8615 (mmm) cc_final: 0.8089 (mmm) REVERT: G 327 GLU cc_start: 0.7842 (tt0) cc_final: 0.7393 (tt0) REVERT: G 341 GLN cc_start: 0.7434 (mt0) cc_final: 0.7136 (mt0) REVERT: G 347 ASP cc_start: 0.7925 (t0) cc_final: 0.7565 (t0) REVERT: G 360 TYR cc_start: 0.8710 (t80) cc_final: 0.8040 (t80) REVERT: G 393 ARG cc_start: 0.8100 (ttt90) cc_final: 0.7314 (tpp80) REVERT: H 28 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7185 (mm110) REVERT: H 48 LEU cc_start: 0.7840 (mt) cc_final: 0.7270 (tt) REVERT: H 67 ASN cc_start: 0.8507 (t0) cc_final: 0.8225 (t0) REVERT: H 97 VAL cc_start: 0.9170 (m) cc_final: 0.8810 (p) REVERT: H 100 GLU cc_start: 0.8536 (pp20) cc_final: 0.8306 (pp20) REVERT: H 104 GLU cc_start: 0.7811 (mt-10) cc_final: 0.6950 (tm-30) REVERT: H 109 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6535 (mm-30) REVERT: H 111 GLU cc_start: 0.3853 (tp30) cc_final: 0.3346 (tp30) REVERT: I 144 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8408 (tm-30) REVERT: I 207 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8479 (tppt) REVERT: I 214 ILE cc_start: 0.8999 (mp) cc_final: 0.8725 (pt) REVERT: I 222 VAL cc_start: 0.9071 (t) cc_final: 0.8818 (t) REVERT: I 243 ASN cc_start: 0.8253 (t0) cc_final: 0.7768 (m-40) REVERT: I 247 VAL cc_start: 0.9043 (t) cc_final: 0.8649 (t) REVERT: J 37 GLU cc_start: 0.8922 (pt0) cc_final: 0.8557 (pm20) REVERT: J 125 HIS cc_start: 0.7555 (m-70) cc_final: 0.7090 (m170) REVERT: J 195 MET cc_start: 0.8850 (mpp) cc_final: 0.8594 (mpp) REVERT: J 251 LEU cc_start: 0.9345 (tp) cc_final: 0.9106 (tp) REVERT: J 257 PHE cc_start: 0.8888 (m-80) cc_final: 0.8687 (m-10) REVERT: J 366 ILE cc_start: 0.9402 (mt) cc_final: 0.9024 (tp) REVERT: J 390 GLU cc_start: 0.8706 (tt0) cc_final: 0.8242 (tm-30) REVERT: J 399 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7505 (pp30) REVERT: J 404 LYS cc_start: 0.8886 (mppt) cc_final: 0.8567 (tppt) REVERT: K 30 LYS cc_start: 0.9442 (tmtt) cc_final: 0.9209 (tttm) REVERT: K 40 ASP cc_start: 0.8874 (p0) cc_final: 0.8603 (p0) REVERT: K 46 GLN cc_start: 0.8170 (tt0) cc_final: 0.7602 (tt0) REVERT: K 104 GLN cc_start: 0.8968 (tp40) cc_final: 0.8712 (tp40) REVERT: K 141 LEU cc_start: 0.9453 (tp) cc_final: 0.9019 (tt) REVERT: K 156 ASP cc_start: 0.8432 (t0) cc_final: 0.7975 (t0) REVERT: K 158 LEU cc_start: 0.8986 (mt) cc_final: 0.8251 (mt) REVERT: K 305 ASP cc_start: 0.8514 (t0) cc_final: 0.8192 (t0) REVERT: K 309 GLU cc_start: 0.8076 (tt0) cc_final: 0.7809 (tt0) REVERT: K 330 TRP cc_start: 0.9286 (t-100) cc_final: 0.8842 (t-100) REVERT: K 400 TYR cc_start: 0.8855 (m-80) cc_final: 0.8587 (m-80) REVERT: L 28 GLN cc_start: 0.7376 (mm110) cc_final: 0.6890 (mm110) REVERT: L 80 ASP cc_start: 0.8751 (t70) cc_final: 0.8436 (t0) REVERT: L 101 ASN cc_start: 0.8766 (t0) cc_final: 0.7775 (m110) REVERT: L 104 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6783 (tm-30) REVERT: L 106 PHE cc_start: 0.7548 (m-80) cc_final: 0.7131 (m-80) REVERT: M 125 CYS cc_start: 0.8072 (t) cc_final: 0.7764 (t) REVERT: M 163 ASP cc_start: 0.8376 (t0) cc_final: 0.8147 (t0) REVERT: M 176 THR cc_start: 0.6314 (m) cc_final: 0.4933 (m) REVERT: M 178 ASP cc_start: 0.8518 (p0) cc_final: 0.8254 (p0) REVERT: M 194 GLU cc_start: 0.7502 (pp20) cc_final: 0.6996 (pp20) REVERT: M 197 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7780 (mmm160) REVERT: M 202 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8229 (ttt90) REVERT: M 220 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8066 (mtm180) REVERT: N 66 LEU cc_start: 0.9137 (mt) cc_final: 0.8542 (mt) REVERT: N 143 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8043 (mtp85) REVERT: N 144 LEU cc_start: 0.8642 (mt) cc_final: 0.8253 (mt) REVERT: N 321 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8771 (mtmm) REVERT: N 396 GLN cc_start: 0.9206 (tt0) cc_final: 0.8991 (tt0) REVERT: O 67 MET cc_start: 0.8517 (tpp) cc_final: 0.8085 (tpp) REVERT: O 80 MET cc_start: 0.9134 (mmp) cc_final: 0.8585 (mmt) REVERT: O 125 THR cc_start: 0.9320 (m) cc_final: 0.8769 (p) REVERT: O 165 TYR cc_start: 0.8536 (p90) cc_final: 0.8325 (p90) REVERT: P 48 LEU cc_start: 0.9444 (mt) cc_final: 0.9240 (mt) REVERT: P 53 PHE cc_start: 0.8635 (t80) cc_final: 0.8424 (t80) REVERT: P 80 ASP cc_start: 0.8648 (m-30) cc_final: 0.8402 (m-30) REVERT: P 93 LEU cc_start: 0.8728 (mt) cc_final: 0.8475 (mt) REVERT: Q 55 THR cc_start: 0.8295 (p) cc_final: 0.8021 (t) REVERT: Q 77 GLU cc_start: 0.8254 (tp30) cc_final: 0.7631 (pt0) REVERT: Q 99 LEU cc_start: 0.9014 (mt) cc_final: 0.8726 (mt) REVERT: R 115 MET cc_start: 0.8647 (mmm) cc_final: 0.8349 (mmm) REVERT: R 125 CYS cc_start: 0.9020 (t) cc_final: 0.8492 (t) REVERT: R 126 VAL cc_start: 0.9304 (m) cc_final: 0.9048 (m) REVERT: R 143 ASN cc_start: 0.6244 (m-40) cc_final: 0.5819 (t0) REVERT: R 160 GLU cc_start: 0.8476 (mp0) cc_final: 0.7863 (mp0) REVERT: R 193 TYR cc_start: 0.8375 (t80) cc_final: 0.8074 (t80) REVERT: R 197 ARG cc_start: 0.9048 (ttm-80) cc_final: 0.8745 (tpp-160) REVERT: R 207 LYS cc_start: 0.9384 (tttm) cc_final: 0.9086 (tptp) REVERT: R 209 ASP cc_start: 0.8349 (m-30) cc_final: 0.7813 (t0) REVERT: R 212 ARG cc_start: 0.8697 (mmt180) cc_final: 0.8262 (mmt-90) REVERT: R 220 ARG cc_start: 0.8540 (ptm160) cc_final: 0.8003 (ptm160) REVERT: R 243 ASN cc_start: 0.8023 (t0) cc_final: 0.7809 (t0) outliers start: 1 outliers final: 0 residues processed: 849 average time/residue: 0.2234 time to fit residues: 310.1730 Evaluate side-chains 731 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 731 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 251 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 382 optimal weight: 0.6980 chunk 381 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 338 optimal weight: 0.9980 chunk 364 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 377 ASN A 396 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS G 341 GLN H 54 GLN J 59 GLN K 33 ASN ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104992 restraints weight = 73894.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108781 restraints weight = 36123.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110183 restraints weight = 19658.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110740 restraints weight = 15542.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110815 restraints weight = 14763.868| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34852 Z= 0.132 Angle : 0.632 16.840 47484 Z= 0.324 Chirality : 0.045 0.186 5340 Planarity : 0.005 0.060 6104 Dihedral : 4.837 27.414 4744 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.13), residues: 4368 helix: 1.68 (0.24), residues: 505 sheet: -0.18 (0.13), residues: 1454 loop : -0.59 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 303 TYR 0.018 0.001 TYR R 175 PHE 0.028 0.001 PHE L 106 TRP 0.043 0.001 TRP M 186 HIS 0.018 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00307 (34800) covalent geometry : angle 0.62755 (47380) SS BOND : bond 0.00371 ( 52) SS BOND : angle 1.66298 ( 104) hydrogen bonds : bond 0.03365 ( 1213) hydrogen bonds : angle 5.14064 ( 3426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7345.05 seconds wall clock time: 127 minutes 29.24 seconds (7649.24 seconds total)